AlignToReferenceBlastDialog Input data Input data Reference Reference Map Sanger Reads to Reference Map Sanger Reads to Reference Input a file with a reference sequence Input a file with a reference sequence ... ... Reads Reads Add Add Remove Remove Settings Settings Mapping min similarity Trimming quality threshold Trimming quality threshold Read name in result alignment Input the result file path Input the result file path % % Mapping min identity Mapping min identity Result alignment Result alignment Add to project Add to project BlastAllSupportDialog Request to Local BLAST Database Request to Local BLAST Database General options General options Select search: Select search: blastn qwe blastn blastp blastp blastx blastx tblastn tblastn tblastx tblastx Search for short, nearly exact matches Search for short, nearly exact matches Expectation value Expectation value Megablast Megablast Off Off Both strands Both strands Direct Direct Complement Complement Base name for BLAST DB files: Base name for BLAST DB files: Number of CPUs being used Number of CPUs being used Advanced options Advanced options Word size Word size Gap costs Gap costs Match scores Match scores 1 -3 1 -3 1 -4 1 -4 1 -2 1 -2 1 -1 1 -1 2 -7 2 -7 2 -5 2 -5 2 -3 2 -3 4 -5 4 -5 5 -4 5 -4 Matrix Matrix gpu-blastp gpu-blastp Database path: Database path: Select a database file Select a database file BLOSUM62 BLOSUM62 BLOSUM45 BLOSUM45 BLOSUM80 BLOSUM80 PAM30 PAM30 PAM70 PAM70 Service Service Max hits: Max hits: plain plain psi psi phi phi PHI pattern PHI pattern Threshold for extending hits Threshold for extending hits Threshold Threshold Composition-based statistics Composition-based statistics D or d: default (equivalent to 2 ) D or d: default (equivalent to 2 ) 0 or F or f: No composition-based statistics 0 or F or f: No composition-based statistics 1: Composition-based statistics as in NAR 29:2994-3005, 2001 1: Composition-based statistics as in NAR 29:2994-3005, 2001 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Filters Filters Low complexity filter Low complexity filter Human repeats filter Human repeats filter Masks Masks Mask for lookup table only Mask for lookup table only Mask lower case letters Mask lower case letters Extension options Extension options X dropoff value (in bits) X dropoff value (in bits) For gapped alignment For gapped alignment For ungapped extensions For ungapped extensions For final gapped alignment For final gapped alignment Multiple Hits window size Multiple Hits Window Size Perform gapped alignment Perform gapped alignment BlastDBCmdDialog Fetch Sequences from BLAST Database Fetch Sequences from BLAST Database Query ID Query ID Select database Select database Output path Output path Entery query ID: Enter query ID: Select database : Select database : ... ... Type of file(s) Type of file(s) nucleotide nucleotide protein protein Output path: Output path: Add to project Add to project BlastDBSelectorWidget Form Form Database path Database path Database file Database file Base name for BLAST DB files Base name for BLAST DB files Database path: Database path: Select a database file Select a database file Base name for BLAST DB files: Base name for BLAST DB files: Bowtie2Settings Parameters Parameters <html><head/><body>By default, Bowtie2 performs end-to-end read alignment. That is, it searches for alignments involving all of the read characters. This is also called an "untrimmed" or "unclipped" alignment.When the --local option is specified, Bowtie2 performs local read alignment. In this mode, Bowtie2 might "trim" or "clip" some read characters from one or both ends of the alignment if doing so maximizes the alignment score.</body></html> <html><head/><body>By default, Bowtie2 performs end-to-end read alignment. That is, it searches for alignments involving all of the read characters. This is also called an "untrimmed" or "unclipped" alignment.When the --local option is specified, Bowtie2 performs local read alignment. In this mode, Bowtie2 might "trim" or "clip" some read characters from one or both ends of the alignment if doing so maximizes the alignment score.</body></html> Mode Mode --end-to-end --end-to-end --local --local <html><head/><body>"Pads" dynamic programming problems by specified number of columns on either side to allow gaps.</body></html> <html><head/><body>"Pads" dynamic programming problems by specified number of columns on either side to allow gaps.</body></html> Add columns to allow gaps (--dpad) Add columns to allow gaps (--dpad) <html><head/><body>Sets the number of mismatches to allowed in a seed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity.</body></html> <html><head/><body>Sets the number of mismatches to allowed in a seed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity.</body></html> <html><head/><body>Launch specified number of parallel search threads. Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear.</body></html> <html><head/><body>Launch specified number of parallel search threads. Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear.</body></html> <html><head/><body>Disallow gaps within specified number of positions of the beginning or end of the read.</body></html> <html><head/><body>Disallow gaps within specified number of positions of the beginning or end of the read.</body></html> <html><head/><body>Use specified value as the seed for pseudo-random number generator.</body></html> <html><head/><body>Use specified value as the seed for pseudo-random number generator.</body></html> Seed (--seed) Seed (--seed) Number of mismatches Number of mismatches Threads Threads <html><head/><body>Sets the length of the seed substrings to align. Smaller values make alignment slower but more senstive.</body></html> <html><head/><body>Sets the length of the seed substrings to align. Smaller values make alignment slower but more senstive.</body></html> Seed length (--L) Seed length (--L) Disallow gaps (--gbar) Disallow gaps (--gbar) Flags Flags <html><head/><body>If Bowtie2 cannot find a paired-end alignment for a pair, by default it will go on to look for unpaired alignments for the constituent mates. This is called "mixed mode." To disable mixed mode, set this option.Bowtie2 runs a little faster in the mixed mode, but will only consider alignment status of pairs per se, not individual mates.</body></html> <html><head/><body>If Bowtie2 cannot find a paired-end alignment for a pair, by default it will go on to look for unpaired alignments for the constituent mates. This is called "mixed mode." To disable mixed mode, set this option.Bowtie2 runs a little faster in the mixed mode, but will only consider alignment status of pairs per se, not individual mates.</body></html> No unpaired alignments (--no-mixed) No unpaired alignments (--no-mixed) <html><head/><body>By default, Bowtie2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints. This option disables that behavior.</body></html> <html><head/><body>By default, Bowtie2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints. This option disables that behavior.</body></html> No discordant alignments (--no-discordant) No discordant alignments (--no-discordant) <html><head/><body>If this option is selected, Bowtie2 will not attempt to align against the forward reference strand.</body></html> <html><head/><body>If this option is selected, Bowtie2 will not attempt to align against the forward reference strand.</body></html> No forward orientation (--nofw) No forward orientation (--nofw) <html><head/><body>If this option is selected, Bowtie2 will not attempt to align against the reverse-complement reference strand.</body></html> <html><head/><body>If this option is selected, Bowtie2 will not attempt to align against the reverse-complement reference strand.</body></html> No reverse-complement orientation (--norc) No reverse-complement orientation (--norc) <html><head/><body>If one mate alignment overlaps the other at all, consider that to be non-concordant. Default: mates can overlap in a concordant alignment.</body></html> <html><head/><body>If one mate alignment overlaps the other at all, consider that to be non-concordant. Default: mates can overlap in a concordant alignment.</body></html> No overlapping mates (--no-overlap) No overlapping mates (--no-overlap) <html><head/><body>If one mate alignment contains the other, consider that to be non-concordant. Default: a mate can contain the other in a concordant alignment.</body></html> <html><head/><body>If one mate alignment contains the other, consider that to be non-concordant. Default: a mate can contain the other in a concordant alignment.</body></html> No mates containing one another (--no-contain) No mates containing one another (--no-contain) BowtieBuildSettings Form Form Colorspace Colorspace BowtieSettings Parameters Parameters <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds quality values to the nearest 10 and saturates at 30; rounding can be disabled with --nomaqround.</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds quality values to the nearest 10 and saturates at 30; rounding can be disabled with --nomaqround.</body></html> Maq error (--maqerr) Maq error (--maqerr) <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> The "seed length"; i.e., the number of bases on the high-quality end of the read to which the -n ceiling applies. The lowest permitted setting is 5 and the default is 28. bowtie is faster for larger values of -l.</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> The "seed length"; i.e., the number of bases on the high-quality end of the read to which the -n ceiling applies. The lowest permitted setting is 5 and the default is 28. bowtie is faster for larger values of -l.</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. Default: 250.</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. Default: 250.</body></html> The number of megabytes of memory a given thread is given to store path descriptors in --best mode. Best-first search must keep track of many paths at once to ensure it is always extending the path with the lowest cumulative cost. Bowtie tries to minimize the memory impact of the descriptors, but they can still grow very large in some cases. If you receive an error message saying that chunk memory has been exhausted in --best mode, try adjusting this parameter up to dedicate more memory to the descriptors. Default: 64. The number of megabytes of memory a given thread is given to store path descriptors in --best mode. Best-first search must keep track of many paths at once to ensure it is always extending the path with the lowest cumulative cost. Bowtie tries to minimize the memory impact of the descriptors, but they can still grow very large in some cases. If you receive an error message saying that chunk memory has been exhausted in --best mode, try adjusting this parameter up to dedicate more memory to the descriptors. Default: 64. Use <int> as the seed for pseudo-random number generator Use <int> as the seed for pseudo-random number generator Mode: Mode: <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> When the -n option is specified (which is the default), bowtie determines which alignments are valid according to the following policy, which is similar to Maq's default policy. In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option. Quality values are ignored. The -v option is mutually exclusive with the -n option.</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> When the -n option is specified (which is the default), bowtie determines which alignments are valid according to the following policy, which is similar to Maq's default policy. In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option. Quality values are ignored. The -v option is mutually exclusive with the -n option.</body></html> -n mode -n mode -v mode -v mode Seed length (--seedlen) Seed length (--seedlen) Maximum of backtracks (--maxbts) Maximum of backtracks (--maxbts) Descriptors memory usage (--chunkmbs) Descriptors memory usage (--chunkmbs) Seed (--seed) Seed (--seed) Threads Threads Flags Flags Colorspace (--color) Colorspace (--color) No Maq rounding (--nomaqround) No Maq rounding (--nomaqround) No forward orientation (--nofw) No forward orientation (--nofw) No reverse-complement orientation (--norc) No reverse-complement orientation (--norc) Try as hard (--tryhard) Try as hard (--tryhard) Best alignments (--best) Best alignments (--best) All alignments (--all) All alignments (--all) <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way. --nomaqround prevents this rounding in bowtie.</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way. --nomaqround prevents this rounding in bowtie.</body></html> If --nofw is specified, bowtie will not attempt to align against the forward reference strand. If --nofw is specified, bowtie will not attempt to align against the forward reference strand. If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand. If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand. <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Try as hard as possible to find valid alignments when they exist, including paired-end alignments. This is equivalent to specifying very high values for the --maxbts and --pairtries options. This mode is generally much slower than the default settings, but can be useful for certain problems. This mode is slower when (a) the reference is very repetitive, (b) the reads are low quality, or (c) not many reads have valid alignments.</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> Try as hard as possible to find valid alignments when they exist, including paired-end alignments. This is equivalent to specifying very high values for the --maxbts and --pairtries options. This mode is generally much slower than the default settings, but can be useful for certain problems. This mode is slower when (a) the reference is very repetitive, (b) the reads are low quality, or (c) not many reads have valid alignments.</body></html> Make Bowtie guarantee that reported singleton alignments are "best" in terms of stratum (i.e. number of mismatches, or mismatches in the seed in the case of -n mode) and in terms of the quality values at the mismatched position(s). bowtie is somewhat slower when --best is specified. Make Bowtie guarantee that reported singleton alignments are "best" in terms of stratum (i.e. number of mismatches, or mismatches in the seed in the case of -n mode) and in terms of the quality values at the mismatched position(s). bowtie is somewhat slower when --best is specified. Report all valid alignments per read or pair. Report all valid alignments per read or pair. BwaBuildSettings Form Form Index algorithm (-a) Index algorithm (-a) autodetect autodetect bwtsw bwtsw div div is is BwaMemSettings Form Form Base Options Base Options Penalty for a mismatch Penalty for a mismatch Score for a sequence match Score for a sequence match Score for a match (-A) Score for a match (-A) Mismatch penalty (-B) Mismatch penalty (-B) Gap open penalty (-O) Gap open penalty (-O) Penalty for an unpaired read pair Penalty for an unpaired read pair Minimum score to output Minimum score to output Penalty unpaired (-U) Penalty unpaired (-U) Penalty for clipping Penalty for clipping Gap open penalty Gap open penalty Gap extension penalty; a gap of size k cost {-O} + {-E}*k Gap extension penalty; a gap of size k cost {-O} + {-E}*k Penalty for clipping (-L) Penalty for clipping (-L) Gap extention penalty (-E) Gap extention penalty (-E) Score threshold (-T) Score threshold (-T) Internall seeds length (-r) Internall seeds length (-r) Min seed length (-k) Min seed length (-k) Look for internal seeds inside a seed longer than {-k} * FLOAT Look for internal seeds inside a seed longer than {-k} * FLOAT Number of threads Number of threads Off-diagonal X-dropoff Off-diagonal X-dropoff Band width for banded alignment Band width for banded alignment Band width (-w) Band width (-w) Minimum seed length Minimum seed length Number of threads (-t) Number of threads (-t) Dropoff (-d) Dropoff (-d) Skip seeds threshold (-c) Skip seeds threshold (-c) Skip seeds with more than INT occurrences Skip seeds with more than INT occurrences Drop chain threshold (-D) Drop chain threshold (-D) Drop chains shorter than FLOAT fraction of the longest overlapping chain Drop chains shorter than FLOAT fraction of the longest overlapping chain Algorithm Internal seeds length (-r) Scoring Options Other Index algorithm (-a) Index algorithm (-a) autodetect autodetect bwtsw bwtsw div div is is Matching score (-A) Matching score (-A) Rounds of mate rescues (-m) Rounds of mate rescues (-m) Perform at most INT rounds of mate rescues for each read Perform at most INT rounds of mate rescues for each read Skip mate rescue Skip mate rescue Skip mate rescue (-S) Skip mate rescue (-S) Skip pairing; mate rescue performed unless -S also in use Skip pairing; mate rescue performed unless -S also in use Skip pairing (-P) Skip pairing (-P) <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> </body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> </body></html> BwaSettings Form Form Best hits (-R) Best hits (-R) Max gap extensions (-e) Max gap extensions (-e) Indel offset (-i) Indel offset (-i) Max long deletion extensions (-d) Max long deletion extensions (-d) Seed length (-l) Seed length (-l) Max seed differences (-k) Max seed differences (-k) Max queue entries (-m) Max queue entries (-m) Enable long gaps Enable long gaps Missing prob (-n) Missing prob (-n) Max #diff (-n) Max #diff (-n) Long-scaled gap penalty for long deletions (-L) Long-scaled gap penalty for long deletions (-L) Advanced Advanced Gap open penalty (-O) Gap open penalty (-O) Barcode length (-B) Barcode length (-B) Quality threshold (-q) Quality threshold (-q) Mismatch penalty (-M) Mismatch penalty (-M) Gap extension penalty (-E) Gap extension penalty (-E) Threads (-t) Threads (-t) Non-iterative mode (-N) Non-iterative mode (-N) Max gap opens (-o) Max gap opens (-o) Base Options Base Options Index algorithm (-a) Index algorithm (-a) autodetect autodetect bwtsw bwtsw div div is is BwaSwSettings Form Form Base Options Base Options Score threshold (divided by match score) (-T) Score threshold (divided by match score) (-T) Number of threads (-t) Number of threads (-t) Number of seeds to start rev alginment (-N) Number of seeds to start rev alginment (-N) Z-best (-z) Z-best (-z) Prefer hard clipping in SAM output (-H) Prefer hard clipping in SAM output (-H) Size of chunk of reads (-s) Size of chunk of reads (-s) Score for a match (-a) Score for a match (-a) Gap extention penalty (-r) Gap extention penalty (-r) Mismatch penalty (-b) Mismatch penalty (-b) autodetect autodetect bwtsw bwtsw div div is is Gap open penalty (-q) Gap open penalty (-q) Band width (-w) Band width (-w) Index algorithm (-a) Index algorithm (-a) Mask level (-c) Mask level (-c) <html><head/><body>Number of seed to trigger reverse alignment</body></html> <html><head/><body>Number of seed to trigger reverse alignment</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> </body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> </body></html> CAP3SupportDialog Contig Assembly with CAP3 Contig Assembly with CAP3 Base Base Input files (long DNA reads to assembly) Input files (long DNA reads to assembly) <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;"> Sequences in FASTA or FASTQ formats are supported. The quality scores for FASTA sequences can be provided in an additional file. The file must be located in the same folder as the original sequences and have the same name as FASTA file, but another extention: .qual</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;"> Sequences in FASTA or FASTQ formats are supported. The quality scores for FASTA sequences can be provided in an additional file. The file must be located in the same folder as the original sequences and have the same name as FASTA file, but another extention: .qual</body></html> Add Add Remove Remove Remove All Remove All Result contig Result contig Path to result contig alignment in ACE format. Path to result contig alignment in ACE format. Clipping for poor regions Clipping for poor regions Base quality cutoff for clipping (-c) Base quality cutoff for clipping (-c) Clipping range (-y) Clipping range (-y) Length and percent identity of an overlap Length and percent identity of an overlap Overlap length cutoff (-o) Overlap length cutoff (-o) Overlap percent identity cutoff (-p) Overlap percent identity cutoff (-p) Quality difference score of an overlap Quality difference score of an overlap Base quality cutoff for differences (-b) Base quality cutoff for differences (-b) Max qscore sum at differences (-d) Max qscore sum at differences (-d) Other parameters Other parameters Max number of word matches (-t) Max number of word matches (-t) Band expansion size (-a) Band expansion size (-a) Max gap length in any overlap (-f) Max gap length in any overlap (-f) Assembly reverse reads (-r) Assembly reverse reads (-r) Similarity score of an overlap Similarity score of an overlap Mismatch score factor (-n) Mismatch score factor (-n) Overlap similarity score cutoff (-s) Overlap similarity score cutoff (-s) Gap penalty factor (-g) Gap penalty factor (-g) Match score factor (-m) Match score factor (-m) ... ... Advanced Advanced ClustalOSupportRunDialog Align with Clustal Omega Align with Clustal Omega Input and output Input and output Input file Input file ... ... Output file Output file Iteration Iteration Number of iterations Number of iterations Max number guidetree iterations Max number guidetree iterations Max number of HMM iterations Max number of HMM iterations Miscellaneous Miscellaneous Number of CPUs being used Number of CPUs being used Set options automatically Set options automatically ClustalWSupportRunDialog Align with ClustalW Align with ClustalW Input and output Input and output Input file Input file ... ... Output file Output file Advanced options Advanced options Gap opening penalty Gap opening penalty Gap extension penalty Gap extension penalty Weight matrix Weight matrix IUB IUB CLUSTALW CLUSTALW Max iterations Max iterations NONE NONE TREE TREE ALIGNMENT ALIGNMENT Iteration type Iteration type Out sequences order Out sequences order Input Input Aligned Aligned Protein gap parameters Protein gap parameters Gap separation distance Gap separation distance Residue-specific gaps off Residue-specific gaps off Hydrophilic gaps off Hydrophilic gaps off No end gap separation penalty No end gap separation penalty ETSSettingsWidget Resource settings Resource settings You can select path for You can select path for Check lastest version of external tools package Check latest version of external tools package <a href="http://ugene.net/external.html">external tools package</a> <a href="http://ugene.net/external.html">external tools package</a> Browse... Browse... Supported tools Supported tools Name Name Path Path Additional information Additional information <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;"> Select an external tool to view more information about it.</body></html> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;"> Select an external tool to view more information about it.</body></html> Binary path: Binary path: Version info Version info FormatDBSupportRunDialog Format Database Format Database Input data Input data Select input file(s) for formatting database: Select input file(s) for formatting database: ... ... Or select folder with input files: Or select folder with input files: Or select directory with input files: File filter File filter Include files filter Include files filter *.fa;*.fasta *.fa;*.fasta Exclude files filter Exclude files filter *.pal *.pal Type of file(s) Type of file(s) protein protein nucleotide nucleotide Output settings Output settings Select the path to save the database into: Select the path to save the database into: Base name for BLAST files: Base name for BLAST files: Title for database file: Title for database file: HmmerBuildDialog HMM3 Build Input and output Input and output Input alignment file ... ... Build to profile Construction strategies assign cols w/ >= symfrac residues as consensus fast Sym fraction Manual construction Hand (requires reference annotation) Tag sequence as a fragment, if L < x*<L>, where x is: Relative weighting Henikoff position-based weights Gerstein/Sonnhammer/Chothia tree weights Henikoff simple filter weights Identity cutoff Skip relative weighting; set all to 1 Use weights given in alignment file Effective weighting Adjust effective sequence number to achieve relative entropy target Minimum relative entropy/position Sigma parameter Use number of single linkage clusters as effective Fractional identity cutoff Use number of sequences as effective Effective sequence number for all models to E-value calibration Length of sequences for MSV Gumbel mu fit Number of sequences for MSV Gumbel mu fit Length of sequences for Viterbi Gumbel mu fit Number of sequences for Viterbi Gumbel mu fit Length of sequences for Forward exp tail mu fit Number of sequences for Forward exp tail mu fit Tail mass for Forward exponential tail mu fit Other Random generator seed * 0 means that one-time arbitrary seed will be used HmmerSearchDialog HMM3 Search Input and output Input and output Query HMM file: ... ... Reporting thresholds Report domains with E-value less than 1E+ Report domains with score greater than Score threshold: Use profile's GA gathering cutoffs Use profile's NC noise cutoffs Use profile's TC trusted cutoffs Number of significant sequences for domain E-value calculation Acceleration heuristics Turn off composition bias filter Turn off biased composition score corrections Turn all heuristic filters off (less speed, more power) MSV filter threshold: Viterbi filter threshold: Forward filter threshold: Other Random generator seed * 0 means that one-time arbitrary seed will be used IntegralBusPort One of these slots must be not empty: '%1', '%2' One of these slots must be not empty: '%1', '%2' Only one of these slots must be binded: '%1', '%2' Only one of these slots must be binded: '%1', '%2' The slot must be not empty: '%1' The slot must be not empty: '%1' Error! One of these slots must be not empty: '%1', '%2' Error! One of these slots must be not empty: '%1', '%2' Error! You can not bind one of sequences slots and one of url slots simultaneously Error! You can not bind one of sequences slots and one of url slots simultaneously '%1' slot must be not binded '%1' slot must be not binded MAFFTSupportRunDialog Align with MAFFT Align with MAFFT Input and output Input and output Input file Input file ... ... Output file Output file Advanced options Advanced options Gap opening penalty Gap opening penalty Offset (works like gap extension penalty) Offset (works like gap extension penalty) Maximum number of iterative refinement Maximum number of iterative refinement MrBayesDialog MrBayes Settings MrBayes Settings Model Model ModelType ModelType Rate Rate Gamma Gamma MCMC MCMC Chain length Chain length Subsampling frequence Subsampling frequence Burn-in length Burn-in length Heated chains Heated chains Heated chain temp Heated chain temp Random seed Random seed Display Options Display Options PhmmerSearchDialog Phmmer Search Input and output Input and output Query sequence file: ... ... Reporting tresholds Report domains with E-value less than 1E+ Report domains with score greater than Number of significant sequences for domain E-value calculation Scoring system Gap open probability Gap extend probability Acceleration Turn off composition bias filter Turn off biased composition score corrections Turn all heuristic filters off (less speed, more power) Viterbi filter treshold MSV filter treshold Forward filter treshold E-value calibration Length of sequences for MSV Gumbel mu fit Number of sequences for MSV Gumbel mu fit Length of sequences for Viterbi Gumbel mu fit Number of sequences for Viterbi Gumbel mu fit Length of sequences for Forward exp tail mu fit Number of sequences for Forward exp tail mu fit Tail mass for Forward exponential tail mu fit Other Random generator seed * 0 means that one-time arbitrary seed will be used PhyMLDialog Substitution model Substitution model Equilibrium frequencies Equilibrium frequencies optimized optimized empirical empirical Transition / transversion ratio Transition / transversion ratio Check to set user value. Uncheck to get the maximum likelihood estimate. Check to set user value. Uncheck to get the maximum likelihood estimate. estimated estimated Proportion of invariable sites Proportion of invariable sites Substitution Model Substitution Model Number of substitution rate categories Number of substitution rate categories Set a fixed value or get the maximum likelihood estimate. estimated fixed Gamma shape parameter Gamma shape parameter Branch Support Branch Support Use fast likelihood-based method Use fast likelihood-based method Perform bootstrap Perform bootstrap It is the number of bootstrap replicates. It is the number of bootstrap replicates. Tree Searching Tree Searching ... ... Type of tree improvement Type of tree improvement Set number of random starting tree Set number of random starting tree Optimise tree topology Optimise topology Optimise topology Optimise branch lengths Optimise branch lengths Optimise substitution rate Display Options Display Options QObject Path for temporary files Path for temporary files Path for temporary files not selected. Path for temporary files not selected. Do you want to select it now? Do you want to select it now? Genome sequence slot is not binded : '%1' Genome sequence slot is not binded : '%1' Transcripts slot is not binded : '%1' Transcripts slot is not binded : '%1' Input transcripts Input transcripts Genomic sequence url Genomic sequence url Genomic sequence url [FASTA] Genomic sequence url [FASTA] Transcripts url Transcripts url Transcripts url [GTF] Transcripts url [GTF] Extracted sequences url Extracted sequences url Output sequences Output sequences The url to the output file with the extracted sequences. The url to the output file with the extracted sequences. Extract Transcript Sequences with gffread Extract Transcript Sequences with gffread Extract transcript sequences from the genomic sequence(s) with gffread. Extract transcript sequences from the genomic sequence(s) with gffread. Installed Installed Not installed Not installed Unexpected value '%1' of the library type Unexpected value '%1' of the library type %1 tool's version is undefined, this may cause some compatibility issues %1 tool's version is undefined, this may cause some compatibility issues Bowtie and TopHat tools have incompatible versions. Your TopHat's version is %1, Bowtie's one is %2. The following are considered to be compatible: Bowtie < "0.12.9" and TopHat <= "2.0.8" or Bowtie >= "0.12.9" and TopHat >= "2.0.8.b" Bowtie and TopHat tools have incompatible versions. Your TopHat's version is %1, Bowtie's one is %2. The following are considered to be compatible: Bowtie < "0.12.9" and TopHat <= "2.0.8" or Bowtie >= "0.12.9" and TopHat >= "2.0.8.b" At least two samples are required At least two samples are required Duplicate sample name: Duplicate sample name: No datasets in the sample: No datasets in the sample: NOTE: "is" index algorithm is not supposed to work with reference sequences having size larger than 2 GB. In order to achieve stable BWA performance it is strongly recommend to set the index algorithm to "bwtsw" NOTE: "is" index algorithm is not supposed to work with reference sequences having size larger than 2 GB. In order to achieve stable BWA performance it is strongly recommend to set the index algorithm to "bwtsw" NOTE: "bwtsw" index algorithm is not supposed to work with reference sequences having size smaller than 10 MB. In order to achieve stable BWA performance it is strongly recommend to set the index algorithm to "is" NOTE: "bwtsw" index algorithm is not supposed to work with reference sequences having size smaller than 10 MB. In order to achieve stable BWA performance it is strongly recommend to set the index algorithm to "is" NOTE: "bwtsw" index algorithm is not supposed to work with reference sequences having size smaller than 10 MB. In order to achieve stable BWA performance it is strongly recommend to set the index algorithm to "is" NOTE: "bwtsw" index algorithm is not supposed to work with reference sequences having size smaller than 10 MB. In order to achieve stable BWA performance it is strongly recommend to set the index algorithm to "is" Sequence name from file File name SnpEffDatabaseDialog Select SnpEff Database Search... SpadesSettings Form Form Base Options Base Options Running mode Running mode Error Correction and Assembly Error Correction and Assembly Assembly only Assembly only Error correction only Error correction only k-mer sizes (-k) k-mer sizes (-k) Dataset type Dataset type auto auto Multi Cell Multi Cell Single Cell Single Cell Memory limit GB (-m) Memory limit GB (-m) Number of threads Number of threads Number of threads (-t) Number of threads (-t) TCoffeeSupportRunDialog Align with T-Coffee Align with T-Coffee Input and output Input and output Input file Input file ... ... Output file Output file Advanced options Advanced options Gap opening penalty Gap opening penalty Gap extension penalty Gap extension penalty Number of iterations Number of iterations U2::AlignToReferenceBlastCmdlineTask Map Sanger reads to reference The '%1' reference file doesn't exist. wrong reference format Filtered by quality (%1): wrong output format U2::AlignToReferenceBlastDialog Align Align Map Map Cancel Cancel File name Sequence name from file Select Output File... Select Output File... Error Error Reference sequence is not set. Reference sequence is not set. No reads provided. No reads provided. Output file is not set. Output file is not set. Overwrite the file? Overwrite the file? The result file already exists. Would you like to overwrite it? The result file already exists. Would you like to overwrite it? Unable to delete the file. Unable to delete the file. Open Reference Sequence Open Reference Sequence Select File(s) with Read(s) Select File(s) with Read(s) U2::BedtoolsIntersectAnnotationsByEntityTask Intersect annotations task Intersect annotations task Failed to get IOAdapterFactory Failed to get IOAdapterFactory Result document is NULL Result document is NULL Failed to get BED format Failed to get BED format U2::BedtoolsIntersectTask BedtoolsIntersect task BedtoolsIntersect task No input A URL No input A URL No input B URL(s) No input B URL(s) Output URL is not set Output URL is not set U2::BedtoolsSupport Bedtools: flexible tools for genome arithmetic and DNA sequence analysis. Bedtools: flexible tools for genome arithmetic and DNA sequence analysis. U2::BigWigSupport bedGraphToBigWig: converts bedGrapth to bigWig. bedGraphToBigWig: converts bedGrapth to bigWig. U2::BlastAllSupport The blastall is the old program developed and distributed by the NCBI for running BLAST searches. The NCBI recommends that people start using the programs of the BLAST+ package instead. The blastall is the old program developed and distributed by the NCBI for running BLAST searches. The NCBI recommends that people start using the programs of the BLAST+ package instead. Path for BLAST %1 tool not selected. Path for BLAST %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::BlastAllSupportContext Query with local BLAST... Query with local BLAST... Path for BLAST %1 tool not selected. Path for BLAST %1 tool not selected. Do you want to select it now? Do you want to select it now? Sequence object is NULL Sequence object is NULL U2::BlastAllSupportMultiTask Source file Source file Used databse Used database No any results found No any results found U2::BlastAllSupportRunDialog Database path contains space characters. Database path contains space characters. Database name contains space characters. Database name contains space characters. Wrong parameters for creating annotations Wrong parameters for creating annotations Error Error Cannot create an annotation object. Please check settings Cannot create an annotation object. Please check settings U2::BlastAllSupportTask A problem occurred during doing BLAST. The sequence is no more available. A problem occurred during doing BLAST. The sequence is no more available. Subfolder for temporary files exists. Can not remove this folder. Subfolder for temporary files exists. Can not remove this folder. Subdirectory for temporary files exists. Can not remove this folder. Can not create folder for temporary files. Can not create folder for temporary files. Can not create fake NCBI ini file Can not create fake NCBI ini file Output file not found Output file not found Output file not found. May be %1 tool path '%2' not valid? Output file not found. May be %1 tool path '%2' not valid? Can not remove folder for temporary files. Can not remove folder for temporary files. Incorrect number of fields in line: %1 Incorrect number of fields in line: %1 Can't get location. Start position is absent in [%1] Can't get location. Start position is absent in [%1] Can't get location. End position is absent in [%1] Can't get location. End position is absent in [%1] Can't get hit start location from [%1] Can't get hit start location from [%1] Can't get hit end location from [%1] Can't get hit end location from [%1] Can't get align length from [%1] Can't get align length from [%1] Can't get gaps from [%1] Can't get gaps from [%1] Can't get identity from [%1] Can't get identity from [%1] Can't open output file Can't open output file Can't get Hsp_query-from element Can't get Hsp_query-from element Can't get Hsp_query-to element Can't get Hsp_query-to element Can't get location. Hsp_query-frame[%1] Can't get location. Hsp_query-frame[%1] Can't get identity Can't get identity Can't get gaps Can't get gaps Can't get align length Can't get align length Can't evaluate location Can't evaluate location U2::BlastAllWithExtFileSpecifySupportRunDialog Select input file Select input file Database path contains space characters. Database path contains space characters. Database name contains space characters. Database name contains space characters. This file has the incompatible format for the BLAST+ search. This file has the incompatible format for the BLAST+ search. This file does not contain any sequence. This file does not contain any sequence. Wrong input file Wrong input file Wrong parameters for creating annotations Wrong parameters for creating annotations U2::BlastDBCmdDialog Fetch Fetch Cancel Cancel Select a database file Select a database file Set a result FASTA file name Set a result FASTA file name U2::BlastDBSelectorWidgetController Database path contains space characters. Database path contains space characters. Database name contains space characters. Database name contains space characters. Select a database file Select a database file No alias or index file found for selected database. No alias or index file found for selected database. U2::BlastDbCmdSupport The BlastDBCmd fetches protein or nucleotide sequences from BLAST+ database based on a query. The BlastDBCmd fetches protein or nucleotide sequences from BLAST+ database based on a query. Path for BLAST+ %1 tool not selected. Path for BLAST+ %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::BlastPlusSupport Path for BLAST+ tools not selected. Path for BLAST+ tools not selected. Do you want to select it now? Do you want to select it now? U2::BlastPlusSupportCommonTask A problem occurred during doing BLAST+. The sequence is no more available. A problem occurred during doing BLAST+. The sequence is no more available. The task uses a temporary folder to process the data. The folder path is required not to have spaces. Please set up an appropriate path for the "Temporary files" parameter on the "Directories" tab of the UGENE Application Settings. Subfolder for temporary files exists. Can not remove this folder. Subfolder for temporary files exists. Can not remove this folder. Can not create folder for temporary files. Can not create folder for temporary files. Can not create fake NCBI ini file Can not create fake NCBI ini file Output file not found Output file not found Output file not found. May be %1 tool path '%2' not valid? Output file not found. May be %1 tool path '%2' not valid? There were no hits found for your BLAST search. There were no hits found for your BLAST search. Can not remove folder for temporary files. Can not remove folder for temporary files. Incorrect number of fields in line: %1 Incorrect number of fields in line: %1 Can't get location Can't get location Can't evaluate location Can't evaluate location Can't get hit location Can't get hit location Can't evaluate hit location Can't evaluate hit location Can't get align length Can't get align length Can't get gaps Can't get gaps Can't get identity Can't get identity Can't open output file Can't open output file Can't read output file Can't read output file U2::BlastPlusSupportContext Fetch sequences by 'id' Fetch sequences by 'id' Query with local BLAST+... Query with local BLAST+... Fetch sequences from local BLAST database Fetch sequences from local BLAST database Fetch sequences by 'id' %1 Fetch sequences by 'id' %1 Path for BLAST+ tools not selected. Path for BLAST+ tools not selected. Do you want to select it now? Do you want to select it now? Sequence object is NULL Sequence object is NULL Path for BLAST+ %1 tool not selected. Path for BLAST+ %1 tool not selected. U2::BlastPlusSupportMultiTask Source file Source file Used databse Used database No any results found No any results found U2::BlastPlusSupportRunDialog Database path contains space characters. Database path contains space characters. Database name contains space characters. Database name contains space characters. Do you want to select it now? Do you want to select it now? Path for BLAST+ %1 tool not selected. Path for BLAST+ %1 tool not selected. Wrong parameters for creating annotations Wrong parameters for creating annotations Error Error Cannot create an annotation object. Please check settings Cannot create an annotation object. Please check settings U2::BlastPlusWithExtFileSpecifySupportRunDialog Select input file Select input file Wrong input file Wrong input file Database path contains space characters. Database path contains space characters. Database name contains space characters. Database name contains space characters. This file has the incompatible format for the BLAST+ search. This file has the incompatible format for the BLAST+ search. This file does not contain sequences. This file does not contain sequences. Do you want to select it now? Do you want to select it now? Path for BLAST+ %1 tool not selected. Path for BLAST+ %1 tool not selected. Wrong parameters for creating annotations Wrong parameters for creating annotations U2::BlastRunCommonDialog Restore to default Restore to default Search Search Cancel Cancel Select a database file Select a database file Direct nucleotide alignment Direct nucleotide alignment Direct protein alignment Direct protein alignment Direct protein alignment (on GPU) Direct protein alignment (on GPU) Protein alignment, input nucleotide is translated input protein before the search Protein alignment, input nucleotide is translated input protein before the search Protein alignment, nucleotide database is translated input protein before the search Protein alignment, nucleotide database is translated input protein before the search Protein alignment, both input query and database are translated before the search Protein alignment, both input query and database are translated before the search U2::Bowtie2AlignTask Unknown short reads format %1 Unknown short reads format %1 U2::Bowtie2BuildIndexTask Reference file "%1" does not exist Reference file "%1" does not exist U2::Bowtie2Support Bowtie 2 aligner takes a Bowtie 2 index and a set of sequencing read files and outputs a set of alignments. Bowtie 2 aligner takes a Bowtie 2 index and a set of sequencing read files and outputs a set of alignments. Bowtie 2 build indexer builds a Bowtie index from a set of DNA sequences. It outputs a set of 6 files with suffixes .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2. These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence files are no longer used by Bowtie 2 once the index is built. Bowtie 2 build indexer builds a Bowtie index from a set of DNA sequences. It outputs a set of 6 files with suffixes .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2. These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence files are no longer used by Bowtie 2 once the index is built. Bowtie 2 index inspector extracts information from a Bowtie index about what kind of index it is and what reference sequence were used to build it. Bowtie 2 index inspector extracts information from a Bowtie index about what kind of index it is and what reference sequence were used to build it. U2::BowtieAssembleTask Reference index file "%1" does not exist Reference index file "%1" does not exist Unknown short reads format %1 Unknown short reads format %1 There is not enough memory on the computer! There is not enough memory on the computer! U2::BowtieBuildIndexTask Reference file "%1" does not exist Reference file "%1" does not exist U2::BowtieSupport Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). U2::BwaAlignTask Short reads are not provided Short reads are not provided In paired-end mode it possible to analyze only 2 read sets using BWA In paired-end mode it possible to analyze only 2 read sets using BWA Please, provide same number of files with downstream and upstream reads. Align reads with BWA Multitask Saming reads with BWA Multitask Log is incomplete Log is incomplete Log is incorrect Log is incorrect U2::BwaMemAlignTask Short reads are not provided Short reads are not provided Please, provide same number of files with downstream and upstream reads. Align reads with BWA-MEM Multitask Wrong settings of paired reads. For paired-read alignment by BWA MEM only a single pair of reads is acceptable. Wrong settings of paired reads. For paired-read alignment by BWA MEM only a single pair of reads is acceptable. U2::BwaMemSettingsWidget NOTE: bwa mem accepts reads only in FASTA or FASTQ format. Reads should be compiled into a single file for each mate end. NOTE: bwa mem accepts reads only in FASTA or FASTQ format. Reads should be compiled into a single file for each mate end. U2::BwaSupport Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. U2::BwaSwAlignTask Short reads are not provided Short reads are not provided BWA SW can not align paired reads BWA SW can not align paired reads U2::BwaSwSettingsWidget NOTE: bwa-sw performs alignment of long sequencing reads (Sanger or 454). It accepts reads only in FASTA or FASTQ format. Reads should be compiled into single file. NOTE: bwa-sw performs alignment of long sequencing reads (Sanger or 454). It accepts reads only in FASTA or FASTQ format. Reads should be compiled into single file. U2::BwaTask Multiple read files are not supported by bwa-sw. Please combine your reads into single FASTA file. Multiple read files are not supported by bwa-sw. Please combine your reads into single FASTA file. Please, provide same number of files with downstream and upstream reads. Multiple read files are not supported by bwa-mem. Please combine your reads into single FASTA file. Multiple read files are not supported by bwa-mem. Please combine your reads into single FASTA file. Please, provide two files with paired reads. Please, provide two files with paired reads. U2::CAP3Support CAP3 is a contig assembly program. It allows to assembly long DNA reads (up to 1000 bp). Binaries can be downloaded from http://seq.cs.iastate.edu/cap3.html CAP3 is a contig assembly program. It allows to assembly long DNA reads (up to 1000 bp). Binaries can be downloaded from http://seq.cs.iastate.edu/cap3.html Huang, X. and Madan, A. (1999) Huang, X. and Madan, A. (1999) CAP3: A DNA Sequence Assembly Program, CAP3: A DNA Sequence Assembly Program, Genome Research, 9: 868-877. Genome Research, 9: 868-877. Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::CAP3SupportDialog Run Run List of input files is empty! List of input files is empty! Result contig file name is not set! Result contig file name is not set! Destination file already exists. To overwrite the file, press 'Replace'. To save under other name press 'Cancel' and change name in 'Result contig' field. Destination file already exists. To overwrite the file, press 'Replace'. To save under other name press 'Cancel' and change name in 'Result contig' field. Replace Replace Add Sequences to Assembly Add Sequences to Assembly Set Result Contig File Name Set Result Contig File Name Cancel Cancel ACE format (*.ace) ACE format (*.ace) U2::CAP3SupportTask Output file not found Output file not found Output file not found. May be %1 tool path '%2' not valid? Output file not found. May be %1 tool path '%2' not valid? Output file not found: copy from tmp dir failed. Output file not found: copy from tmp dir failed. U2::CEASSupport CEAS - Cis-regulatory Element Annotation System - helps to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. It provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor. CEAS - Cis-regulatory Element Annotation System - helps to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. It provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor. U2::CEASSupportTask CEAS error: Can not find a required output file %1. CEAS error: Can not find a required output file %1. Can not copy the result file to: %1 Can not copy the result file to: %1 U2::ClustalOSupport Clustal Omega is a free sequence alignment software for proteins. Clustal Omega is a free sequence alignment software for proteins. Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::ClustalOSupportContext Align with ClustalO... Align with ClustalO... Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::ClustalOSupportRunDialog Align Align Cancel Cancel U2::ClustalOSupportTask ClustalO alignment started ClustalO alignment started Saving data to temporary file '%1' Saving data to temporary file '%1' Subfolder for temporary files exists. Can not remove this folder. Subfolder for temporary files exists. Can not remove this folder. Can not create folder for temporary files. Can not create folder for temporary files. Output file %1 not found Output file %1 not found Output file %3 not found. May be %1 tool path '%2' not valid? Output file %3 not found. May be %1 tool path '%2' not valid? Loading output file '%1' Loading output file '%1' Failed to apply the result of ClustalO: alignment object is not available! Failed to apply the result of ClustalO: alignment object is not available! ClustalO alignment successfully finished ClustalO alignment successfully finished Can not remove folder for temporary files. Can not remove folder for temporary files. U2::ClustalOWithExtFileSpecifySupportRunDialog Align Align Cancel Cancel Open an alignment file Open an alignment file Save an multiple alignment file Save an multiple alignment file Kalign with Align Align with Kalign Input file is not set! Input file is not set! Output file is not set! Output file is not set! U2::ClustalOWithExtFileSpecifySupportTask Unrecognized input alignment file format Unrecognized input alignment file format U2::ClustalWSupport ClustalW is a free sequence alignment software for DNA or proteins. ClustalW is a free sequence alignment software for DNA or proteins. Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::ClustalWSupportContext Align with ClustalW... Align with ClustalW... Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::ClustalWSupportRunDialog Align Align Cancel Cancel U2::ClustalWSupportTask Unsupported alphabet: %1 Unsupported alphabet: %1 ClustalW alignment started ClustalW alignment started Saving data to temporary file '%1' Saving data to temporary file '%1' Output file %1 not found Output file %1 not found Output file %3 not found. May be %1 tool path '%2' not valid? Output file %3 not found. May be %1 tool path '%2' not valid? Loading output file '%1' Loading output file '%1' Failed to apply the result of ClustalW: alignment object is not available! Failed to apply the result of ClustalW: alignment object is not available! ClustalW alignment successfully finished ClustalW alignment successfully finished Can not remove folder for temporary files. Can not remove folder for temporary files. U2::ClustalWWithExtFileSpecifySupportRunDialog Align Align Cancel Cancel Open an alignment file Open an alignment file Save an multiple alignment file Save an multiple alignment file Kalign with Align Align with Kalign Input file is not set! Input file is not set! Output file is not set! Output file is not set! U2::ClustalWWithExtFileSpecifySupportTask Unrecognized input alignment file format Unrecognized input alignment file format U2::ConductGOSupport Conduct GO - For a list of input genes, this tool uses R/BioC packages (GO, GOstats) to identify over represented GO terms. Conduct GO - For a list of input genes, this tool uses R/BioC packages (GO, GOstats) to identify over represented GO terms. U2::ConductGOTask Conduct GO warning: Can not find a required output file %1. Conduct GO warning: Can not find a required output file %1. Can not copy the result file to: %1 Can not copy the result file to: %1 U2::ConservationPlotSupport ConservationPlot - Draw conservation plot for many bed files. ConservationPlot - Draw conservation plot for many bed files. U2::ConservationPlotTask An annotation table object wasn't found in the workflow data storage An annotation table object wasn't found in the workflow data storage Conservation Plot error: Can not find a required output file %1. Conservation Plot error: Can not find a required output file %1. Can not copy the result file to: %1 Can not copy the result file to: %1 U2::ConvertAlignment2Stockholm Convert alignment to Stockholm format Cannot create a folder for temporary files. File doesn't contain any multiple alignments. File contains several multiple alignments. Only the first one is saved to the result file. U2::CopyFileTask Copy file task Copy file task Input file is not set Input file is not set Output file is not set Output file is not set Copy %1 to %2 Copy %1 to %2 Can not rename existing file '%1' Can not rename existing file '%1' Error copying file Error copying file File copying finished File copying finished File copying task was finished with an error: %1 File copying task was finished with an error: %1 File copy was finished. Copy of '%1' is '%2' File copy was finished. Copy of '%1' is '%2' U2::CuffdiffSupportTask Running Cuffdiff task Running Cuffdiff task Workflow data storage is NULL Workflow data storage is NULL At least 2 sets of assemblies are required for Cuffdiff At least 2 sets of assemblies are required for Cuffdiff U2::CufflinksSupport Cuffcompare helps comparing assembled transcripts to a reference annotation, and also tracking transcripts across multiple experiments. Cuffcompare helps comparing assembled transcripts to a reference annotation, and also tracking transcripts across multiple experiments. Cuffdiff  tests for differential expression and regulation in RNA-Seq samples. Cuffdiff  tests for differential expression and regulation in RNA-Seq samples. Cufflinks assembles transcripts and estimates their abundances. Cufflinks assembles transcripts and estimates their abundances. Cuffmerge merges together several assemblies. Cuffmerge merges together several assemblies. Gffread is used to verify or perform various operations on GFF files. Gffread is used to verify or perform various operations on GFF files. U2::CufflinksSupportTask Running Cufflinks task Running Cufflinks task Unable to get an assembly object. Unable to get an assembly object. An internal error occurred during getting annotations from a %1 output file! An internal error occurred during getting annotations from a %1 output file! U2::CuffmergeSupportTask Running Cuffmerge task Running Cuffmerge task Workflow data storage is NULL Workflow data storage is NULL There are no annotations to process There are no annotations to process Can not create a file: %1 Can not create a file: %1 An internal error occurred during getting annotations from a %1 output file! An internal error occurred during getting annotations from a %1 output file! U2::CutadaptSupport cutadapt removes adapter sequences from high-throughput sequencing data. This is necessary when the reads are longer than the molecule that is sequenced, such as in microRNA data. cutadapt removes adapter sequences from high-throughput sequencing data. This is necessary when the reads are longer than the molecule that is sequenced, such as in microRNA data. U2::ETSProjectViewItemsContoller FormatDB... FormatDB... BLAST+ make DB... BLAST+ make DB... BLAST BLAST Path for BLAST %1 tool not selected. Path for BLAST %1 tool not selected. Path for BLAST+ %1 tool not selected. Path for BLAST+ %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::ExternalToolJustValidateTask Tool's path is empty Tool's path is empty Tool's executable isn't exists Tool's executable isn't exists Scripting tool registry is NULL Scripting tool registry is NULL Scripting tool '%1' isn't found in the registry Scripting tool '%1' isn't found in the registry Tool does not start. It is possible that the specified executable file %1 for %2 tool is invalid. You can change the path to the executable file in the external tool settings in the global preferences. Tool does not start. It is possible that the specified executable file %1 for %2 tool is invalid. You can change the path to the executable file in the external tool settings in the global preferences. Can not find expected message. It is possible that the specified executable file %1 for %2 tool is invalid. You can change the path to the executable file in the external tool settings in the global preferences. Can not find expected message. It is possible that the specified executable file %1 for %2 tool is invalid. You can change the path to the executable file in the external tool settings in the global preferences. U2::ExternalToolSearchAndValidateTask Can not find expected message. It is possible that the specified executable file %1 for %2 tool is invalid. You can change the path to the executable file in the external tool settings in the global preferences. Can not find expected message. It is possible that the specified executable file %1 for %2 tool is invalid. You can change the path to the executable file in the external tool settings in the global preferences. U2::ExternalToolSearchTask '%1' external tool search task '%1' external tool search task An external tool '%1' isn't found in the registry An external tool '%1' isn't found in the registry Tool pointer is NULL Tool pointer is NULL External tool module hasn't any dependencies: it hasn't master tool External tool module hasn't any dependencies: it hasn't master tool External tool registry is NULL External tool registry is NULL Tool's executable name is not set Tool's executable name is not set U2::ExternalToolSupportPlugin Search tools in PATH Search tools in PATH External tool support External tool support Runs other external tools Runs other external tools Align with ClustalW... Align with ClustalW... Align with ClustalO... Align with ClustalO... Align with MAFFT... Align with MAFFT... Align with T-Coffee... Align with T-Coffee... BLAST make database... BLAST make database... BLAST+ make database... BLAST+ make database... Map reads to reference... Map reads to reference... Reads de novo assembly (with %1)... Reads de novo assembly (with %1)... BLAST+ search... BLAST+ search... BLAST+ query database... BLAST+ query database... Contig assembly with %1... Contig assembly with %1... BLAST search... BLAST search... The subfolder for temporary files '%1' already exists. Can not remove this folder! The subfolder for temporary files '%1' already exists. Can not remove this folder! Can not create a subfolder for temporary files '%1'! Can not create a subfolder for temporary files '%1'! U2::ExternalToolSupportService External tools support External tools support Provides support to run external tools from UGENE Provides support to run external tools from UGENE U2::ExternalToolSupportSettingsPageController External Tools External Tools U2::ExternalToolSupportSettingsPageWidget Select an external tool to view more information about it. Select an external tool to view more information about it. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. BLAST+ is a new version of the BLAST package from the NCBI. BLAST+ is a new version of the BLAST package from the NCBI. Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. It also estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. It also estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. It indexes the genome with an FM index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2Gb. Bowtie 2 supports gapped, local, and paired-end alignment modes. Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. It indexes the genome with an FM index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2Gb. Bowtie 2 supports gapped, local, and paired-end alignment modes. Cistrome is a UGENE version of Cistrome pipeline which also includes some tools useful for ChIP-seq analysisThis pipeline is aimed to provide the following analysis steps: peak calling and annotating, motif search and gene ontology. Cistrome is a UGENE version of Cistrome pipeline which also includes some tools useful for ChIP-seq analysis. This pipeline is aimed to provide the following analysis steps: peak calling and annotating, motif search and gene ontology. No description No description External tool '%1' cannot be validated as it depends on other tools, some of which are not valid. The list of tools is the following: External tool '%1' cannot be validated as it depends on other tools, some of which are not valid. The list of tools is the following: '%1' is %2 module and it is not installed. Install it and restart UGENE or set another %2 with already installed '%1' module. '%1' is %2 module and it is not installed. Install it and restart UGENE or set another %2 with already installed '%1' module. Version: Version: unknown unknown Binary path: Binary path: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). <a href='http://qt-project.org/doc/qt-4.8/qtextbrowser.html#anchorClicked'>Link text</a> Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). <a href='http://qt-project.org/doc/qt-4.8/qtextbrowser.html#anchorClicked'>Link text</a> Choose Folder With Executables Choose Folder With Executables Choose Folder With External Tools Pack Choose Folder With External Tools Pack Not a valid external tools folder Not a valid external tools folder U2::ExternalToolUtils Paths for the following tools are not selected: %1. Do you want to select it now? Do you want to select it now? U2::ExternalToolValidateTask %1 validate task %1 validate task U2::ExternalToolsInstallTask Installing external tools Installing external tools failed: failed: U2::ExternalToolsSearchTask Searching external tools Searching external tools failed: failed: U2::ExternalToolsValidateTask Checking external tools Checking external tools failed: failed: U2::FastQCSupport FastQC: A quality control tool for high throughput sequence data. FastQC: A quality control tool for high throughput sequence data. U2::FastQCTask No input URL The input file '%1' is empty. Folder does not exist: %1 Result file does not exist: %1. See the log for details. U2::FormatDBSupport The formatdb formats protein or nucleotide source databases before these databases can be searched by blastall. The formatdb formats protein or nucleotide source databases before these databases can be searched by blastall. The makeblastdb formats protein or nucleotide source databases before these databases can be searched by other BLAST+ tools. The makeblastdb formats protein or nucleotide source databases before these databases can be searched by other BLAST+ tools. Path for BLAST %1 tool not selected. Path for BLAST %1 tool not selected. Path for BLAST+ %1 tool not selected. Path for BLAST+ %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::FormatDBSupportRunDialog Format Format Cancel Cancel Select file(s) Select file(s) Select a folder with input files Select a folder with input files Select a folder to save database files Select a folder to save database files Input files paths contain space characters. Input files paths contain space characters. Output database path contain space characters. Output database path contain space characters. U2::FormatDBSupportTask Run NCBI FormatDB task Run NCBI FormatDB task Cannot create temp folder Trying to initialize Format DB task second time Input files paths contain space characters. Input files paths contain space characters. Output database path contain space characters. Output database path contain space characters. Blast database creation has been cancelled Blast database creation has been cancelled Can not remove folder for temporary files. Can not remove folder for temporary files. Blast database has been successfully created Blast database has been successfully created Source sequences: Source sequences: Database file path: %1 Database file path: %1 Type: %1 Type: %1 Formatdb log file path: Formatdb log file path: Blast database creation has been failed Blast database creation has been failed U2::GTest_CompareHmmFiles File #1 not set File #2 not set Error creating ioadapter for first file Error opening 1 file Error creating ioadapter for second file Error opening second file Names of aligments not matched Comparing files length not matched Files parts not equal:'%1' and '%2' U2::GTest_UHMM3SearchCompare Can't parse significance:%1 Internal error (cannot parse float number from string '%1') U2::GTest_UHMMER3Build No input file given No output file given U2::Gene2PeakFormatLoader Incorrect start position at line %1: '%2' Incorrect end position at line %1: '%2' Incorrect NA value at line %1: '%2' U2::GffreadSupportTask Running Gffread task Running Gffread task Unknown file format: %1 Unknown file format: %1 The file format is not [%1]: %2 The file format is not [%1]: %2 U2::HmmerAdvContext Find HMM signals with HMMER3... Error Error Sequences larger 2Gb are not supported on 32-bit architecture. No sequence in focus found U2::HmmerBuildDialog Build Cancel Cancel Select hmm file to create Select multiple alignment file input file is empty output hmm file is empty Error: bad arguments! U2::HmmerBuildFromFileTask Build HMMER profile from file Msa URL is empty U2::HmmerBuildFromMsaTask Build HMMER profile from msa HMM profile URL is empty Cannot create a folder for temporary files. U2::HmmerBuildTask Source alignment Profile name Options: Model construction strategies Relative model construction strategies Gerstein/Sonnhammer/Chothia tree weights Henikoff simple filter weights Henikoff position-based weights No relative weighting; set all to 1 Weights given in MSA file Effective sequence weighting strategies adjust effective sequence number to achieve relative entropy target effective sequence number is number of single linkage clusters no effective sequence number weighting: just use number of sequences set effective sequence number for all models to: %1 Task finished with error: '%1' Unknown model construction strategy Unknown relative sequence weighting strategy Unknown effective sequence weighting strategy U2::HmmerMsaEditorContext Build HMMER3 profile U2::HmmerParseSearchResultsTask Can't parse line %1 U2::HmmerSearchDialog Run Run Cancel Cancel HMM profile is not set Settings are invalid Error Error Cannot create an annotation object. Please check settings Cannot create an annotation object. Please check settings Error: bad arguments! HMM profile Select query HMM profile U2::HmmerSearchTask HMMER search HMM profile used: Task was not finished Result annotation table: Result annotation group: Result annotation name: Results count: Cannot create a folder for temporary files. Unknown option controlling model-specific thresholding U2::HmmerSupport Error! Target sequence not selected: no opened annotated dna view HMMER build constructs HMM profiles from multiple sequence alignments. Build HMM3 profile... HMMER search searches profile(s) against a sequence database. Search with HMMER3... PHMMER search searches a protein sequence against a protein database. Search with phmmer... Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::JavaSupport Java Platform lets you develop and deploy Java applications on desktops and servers. (Requires Java 1.7 or higher). Java can be freely downloaded on the official web-site: https://www.java.com/en/download/ Java Platform lets you develop and deploy Java applications on desktops and servers. (Requires Java 1.7 or higher). Java can be freely downloaded on the official web-site: https://www.java.com/en/download/ U2::LocalWorkflow::AlignToReferenceBlastPrompter Input sequence Input sequence Input sequence. Aligned data Aligned data. Reference URL A URL to the file with a reference sequence. Result alignment URL An URL to write the result alignment. Mapping min similarity Reads, whose similarity with the reference is less than the stated value, will be ignored. Read name in result alignment Reads in the result alignment can be named either by names of the sequences in the input files or by the input files names. For example, if the sequences have the same name, set this value to "File name" to be able to distinguish the reads in the result alignment. unset unset Aligns each sequence from %1 to the reference sequence from %2. U2::LocalWorkflow::AlignToReferenceBlastTask Map to reference Details Reference sequence: Mapped reads (%1): similarity Filtered by low similarity (%1): U2::LocalWorkflow::AlignToReferenceBlastWorker Map to Reference Align input sequences (e.g. Sanger reads) to the reference sequence. The result file was not produced U2::LocalWorkflow::BaseShortReadsAlignerWorker Not enough upstream reads datasets Not enough downstream reads datasets Output folder Output folder Folder to save output files. Folder to save output files. Reference genome Reference genome Path to indexed reference genome. Path to indexed reference genome. Library Library Is this library mate-paired? Is this library mate-paired? Filter unpaired reads Should the reads be checked for incomplete pairs? Output file name Output file name Base name of the output file. 'out.sam' by default Base name of the output file. 'out.sam' by default URL of a file with reads URL of a file with reads Input reads to be aligned. Input reads to be aligned. URL of a file with mate reads URL of a file with mate reads Input mate reads to be aligned. Input mate reads to be aligned. Input data Input data Reverse FASTQ file Reverse FASTQ file Reverse paired reads to be aligned. Reverse paired reads to be aligned. Assembly URL Assembly URL Output assembly URL. Output assembly URL. Output data Output data Output assembly files. Output assembly files. U2::LocalWorkflow::BedGraphToBigWigPrompter unset unset from %1 from %1 Converts bedGraph files to bigWig %1 with bedGraphToBigWig. Converts bedGraph files to bigWig %1 with bedGraphToBigWig. U2::LocalWorkflow::BedGraphToBigWigWorker Convert bedGraph Files to bigWig Convert bedGraph Files to bigWig Convert bedGraph Files to bigWig. Convert bedGraph Files to bigWig. BedGrapgh files BedGrapgh files Set of bedGraph files Set of bedGraph files BigWig files BigWig files Output folder Output folder Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Custom folder Custom folder Select the custom output folder. Select the custom output folder. Output name Output name A name of an output file. If default of empty value is provided the output name is the name of the first BAM file with an extention. A name of an output file. If default of empty value is provided the output name is the name of the first BAM file with an extention. Block size Block size Number of items to bundle in r-tree (-blockSize). Number of items to bundle in r-tree (-blockSize). Items per slot Items per slot Number of data points bundled at lowest level (-itemsPerSlot). Number of data points bundled at lowest level (-itemsPerSlot). Uncompressed Uncompressed If set, do not use compression (-unc). If set, do not use compression (-unc). Genome Genome File with genome length. File with genome length. Custom Custom Input file Input file Workflow Workflow U2::LocalWorkflow::BedtoolsIntersectPrompter Intersect annotations from %1 (set A) with annotations from %2 (set B). Report Intersect annotations from %1 (set A) with annotations from %2 (set B). Report U2::LocalWorkflow::BedtoolsIntersectWorker Data not found by %1 id Data not found by %1 id Can not get annotation table object Can not get annotation table object Annotations A Annotations A Annotations B Annotations B Annotations Annotations Result annotations Result annotations Minimum overlap Minimum overlap Minimum overlap required as a fraction of an annotation from set A. By default, even 1 bp overlap between annotations from set A and set B is taken into account. Yet sometimes you may want to restrict reported overlaps to cases where the annotations in B overlaps at least X% (e.g. 50%) of the A annotation. Minimum overlap required as a fraction of an annotation from set A. By default, even 1 bp overlap between annotations from set A and set B is taken into account. Yet sometimes you may want to restrict reported overlaps to cases where the annotations in B overlaps at least X% (e.g. 50%) of the A annotation. Select one of the following:<ul><li>Shared interval to report intervals shared between overlapped annotations from set A and set B.</li><li>Overlapped annotations from A to report annotations from set A that have an overlap with annotations from set B.</li><li>Non-overlapped annotations from A to report annotations from set A that have NO overlap with annotations from set B.</li></ul> Select one of the following:<ul><li>Shared interval to report intervals shared between overlapped annotations from set A and set B.</li><li>Overlapped annotations from A to report annotations from set A that have an overlap with annotations from set B.</li><li>Non-overlapped annotations from A to report annotations from set A that have NO overlap with annotations from set B.</li></ul> Unique overlaps Unique overlaps If the parameter value is "True", write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B. The minimum overlap number is ignored in this case. If the parameter value is "False", the A annotation is reported for every overlap found. If the parameter value is "True", write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B. The minimum overlap number is ignored in this case. If the parameter value is "False", the A annotation is reported for every overlap found. Intersect Annotations Intersect Annotations Intersects two sets of annotations denoted as A and B. Intersects two sets of annotations denoted as A and B. U2::LocalWorkflow::BlastAllPrompter unset unset from %1 from %1 For sequence %1 find annotations in database %2. For sequence %1 find annotations in database %2. U2::LocalWorkflow::BlastAllWorker Best hits limit Best hits limit Number of best hits from a region to keep. 0 turns it off. If used, 100 is recommended. Number of best hits from a region to keep. 0 turns it off. If used, 100 is recommended. Input sequence Input sequence Sequence for which annotations is searched. Sequence for which annotations is searched. Annotations Annotations Found annotations. Found annotations. Search type Search type Select type of BLAST searches. Select type of BLAST searches. Database Path Database Path Path with database files. Path with database files. Database Name Database Name Base name for BLAST DB files. Base name for BLAST DB files. Expected value Expected value This setting specifies the statistical significance threshold for reporting matches against database sequences. This setting specifies the statistical significance threshold for reporting matches against database sequences. Annotate as Annotate as Name for annotations. Name for annotations. Tool Path Tool Path External tool path. External tool path. Temporary folder Temporary folder Folder for temporary files. Folder for temporary files. BLAST output BLAST output Location of BLAST output file. Location of BLAST output file. BLAST output type BLAST output type Type of BLAST output file. Type of BLAST output file. Gapped alignment Gapped alignment Perform gapped alignment. Perform gapped alignment. Gap costs Gap costs Cost to create and extend a gap in an alignment. Cost to create and extend a gap in an alignment. Match scores Match scores Reward and penalty for matching and mismatching bases. Reward and penalty for matching and mismatching bases. Local BLAST search Local BLAST search Finds annotations for DNA sequence in local database. Finds annotations for DNA sequence in local database. Empty sequence supplied to BLAST Empty sequence supplied to BLAST Selected BLAST search with nucleotide input sequence Selected BLAST search with nucleotide input sequence Selected BLAST search with amino acid input sequence Selected BLAST search with amino acid input sequence Not selected BLAST output file Not selected BLAST output file U2::LocalWorkflow::BlastPlusPrompter unset unset from %1 from %1 For sequence %1 find annotations in database %2. For sequence %1 find annotations in database %2. U2::LocalWorkflow::BlastPlusWorker Culling limit Culling limit If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit Input sequence Input sequence Sequence for which annotations is searched. Sequence for which annotations is searched. Annotations Annotations Found annotations. Found annotations. Search type Search type Select type of BLAST+ searches. Select type of BLAST+ searches. Database Path Database Path Path with database files. Path with database files. Database Name Database Name Base name for BLAST+ DB files. Base name for BLAST+ DB files. Expected value Expected value This setting specifies the statistical significance threshold for reporting matches against database sequences. This setting specifies the statistical significance threshold for reporting matches against database sequences. Composition-based statistics Composition-based statistics Composition-based statistics. Composition-based statistics. Annotate as Annotate as Name for annotations. Name for annotations. Tool Path Tool Path External tool path. External tool path. Temporary folder Temporary folder Folder for temporary files. Folder for temporary files. BLAST output BLAST output Location of BLAST output file. Location of BLAST output file. BLAST output type BLAST output type Type of BLAST output file. Type of BLAST output file. Gapped alignment Gapped alignment Perform gapped alignment. Perform gapped alignment. Gap costs Gap costs Cost to create and extend a gap in an alignment. Cost to create and extend a gap in an alignment. Match scores Match scores Reward and penalty for matching and mismatching bases. Reward and penalty for matching and mismatching bases. Local BLAST+ Search Local BLAST+ Search Finds annotations for DNA sequence in local database. Finds annotations for DNA sequence in local database. Empty sequence supplied to BLAST Empty sequence supplied to BLAST Selected BLAST search with nucleotide input sequence Selected BLAST search with nucleotide input sequence Selected BLAST search with amino acid input sequence Selected BLAST search with amino acid input sequence Not selected BLAST output file Not selected BLAST output file U2::LocalWorkflow::Bowtie2Worker Mode Mode When the -n option is specified (which is the default), bowtie determines which alignments are valid according to the following policy, which is similar to Maq's default policy. In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option. Quality values are ignored. The -v option is mutually exclusive with the -n option. When the -n option is specified (which is the default), bowtie determines which alignments are valid according to the following policy, which is similar to Maq's default policy. In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option. Quality values are ignored. The -v option is mutually exclusive with the -n option. Number of mismatches Number of mismatches Sets the number of mismatches to allowed in a seed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Sets the number of mismatches to allowed in a seed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Seed length (--L) Seed length (--L) Sets the length of the seed substrings to align. Smaller values make alignment slower but more senstive. Sets the length of the seed substrings to align. Smaller values make alignment slower but more senstive. Add columns to allow gaps (--dpad) Add columns to allow gaps (--dpad) "Pads" dynamic programming problems by specified number of columns on either side to allow gaps. "Pads" dynamic programming problems by specified number of columns on either side to allow gaps. Disallow gaps (--gbar) Disallow gaps (--gbar) Disallow gaps within specified number of positions of the beginning or end of the read. Disallow gaps within specified number of positions of the beginning or end of the read. Seed (--seed) Seed (--seed) Use specified value as the seed for pseudo-random number generator. Use specified value as the seed for pseudo-random number generator. Threads Threads Launch specified number of parallel search threads. Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear. Launch specified number of parallel search threads. Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear. No unpaired alignments (--no-mixed) No unpaired alignments (--no-mixed) If Bowtie2 cannot find a paired-end alignment for a pair, by default it will go on to look for unpaired alignments for the constituent mates. This is called "mixed mode." To disable mixed mode, set this option. Bowtie2 runs a little faster in the mixed mode, but will only consider alignment status of pairs per se, not individual mates. If Bowtie2 cannot find a paired-end alignment for a pair, by default it will go on to look for unpaired alignments for the constituent mates. This is called "mixed mode." To disable mixed mode, set this option. Bowtie2 runs a little faster in the mixed mode, but will only consider alignment status of pairs per se, not individual mates. No discordant alignments (--no-discordant) No discordant alignments (--no-discordant) By default, Bowtie2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints. This option disables that behavior. By default, Bowtie2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints. This option disables that behavior. No forward orientation (--nofw) No forward orientation (--nofw) If --nofw is specified, bowtie will not attempt to align against the forward reference strand. If --nofw is specified, bowtie will not attempt to align against the forward reference strand. No reverse-complement orientation (--norc) No reverse-complement orientation (--norc) If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand. If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand. No overlapping mates (--no-overlap) No overlapping mates (--no-overlap) If one mate alignment overlaps the other at all, consider that to be non-concordant. Default: mates can overlap in a concordant alignment. If one mate alignment overlaps the other at all, consider that to be non-concordant. Default: mates can overlap in a concordant alignment. No mates containing one another (--no-contain) No mates containing one another (--no-contain) If one mate alignment contains the other, consider that to be non-concordant. Default: a mate can contain the other in a concordant alignment. If one mate alignment contains the other, consider that to be non-concordant. Default: a mate can contain the other in a concordant alignment. Align Reads with Bowtie2 Align Reads with Bowtie2 Performs alignment of short reads with Bowtie2. Performs alignment of short reads with Bowtie2. U2::LocalWorkflow::BowtieWorker Mode: Mode: When the -n option is specified (which is the default), bowtie determines which alignments are valid according to the following policy, which is similar to Maq's default policy. In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option. Quality values are ignored. The -v option is mutually exclusive with the -n option. When the -n option is specified (which is the default), bowtie determines which alignments are valid according to the following policy, which is similar to Maq's default policy. In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option. Quality values are ignored. The -v option is mutually exclusive with the -n option. Mismatches number Mismatches number Mismatches number. Mismatches number. Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed. The default is 70. Like Maq, bowtie rounds quality values to the nearest 10 and saturates at 30; rounding can be disabled with --nomaqround. Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed. The default is 70. Like Maq, bowtie rounds quality values to the nearest 10 and saturates at 30; rounding can be disabled with --nomaqround. Seed length Seed length The seed length; i.e., the number of bases on the high-quality end of the read to which the -n ceiling applies. The lowest permitted setting is 5 and the default is 28. bowtie is faster for larger values of -l. The seed length; i.e., the number of bases on the high-quality end of the read to which the -n ceiling applies. The lowest permitted setting is 5 and the default is 28. bowtie is faster for larger values of -l. No forward orientation No forward orientation If --nofw is specified, bowtie will not attempt to align against the forward reference strand. If --nofw is specified, bowtie will not attempt to align against the forward reference strand. No reverse-complement orientation No reverse-complement orientation If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand. If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand. Maximum of backtracks Maximum of backtracks The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. Default: 250. The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. Default: 250. Try as hard Try as hard Try as hard as possible to find valid alignments when they exist, including paired-end alignments. This is equivalent to specifying very high values for the --maxbts and --pairtries options. This mode is generally much slower than the default settings, but can be useful for certain problems. This mode is slower when (a) the reference is very repetitive, (b) the reads are low quality, or (c) not many reads have valid alignments. Try as hard as possible to find valid alignments when they exist, including paired-end alignments. This is equivalent to specifying very high values for the --maxbts and --pairtries options. This mode is generally much slower than the default settings, but can be useful for certain problems. This mode is slower when (a) the reference is very repetitive, (b) the reads are low quality, or (c) not many reads have valid alignments. Best hits Best hits The number of megabytes of memory a given thread is given to store path descriptors in --best mode. Best-first search must keep track of many paths at once to ensure it is always extending the path with the lowest cumulative cost. Bowtie tries to minimize the memory impact of the descriptors, but they can still grow very large in some cases. If you receive an error message saying that chunk memory has been exhausted in --best mode, try adjusting this parameter up to dedicate more memory to the descriptors. Default: 64. The number of megabytes of memory a given thread is given to store path descriptors in --best mode. Best-first search must keep track of many paths at once to ensure it is always extending the path with the lowest cumulative cost. Bowtie tries to minimize the memory impact of the descriptors, but they can still grow very large in some cases. If you receive an error message saying that chunk memory has been exhausted in --best mode, try adjusting this parameter up to dedicate more memory to the descriptors. Default: 64. No Maq rounding No Maq rounding Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way. --nomaqround prevents this rounding in bowtie. Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way. --nomaqround prevents this rounding in bowtie. Seed Seed Use <int> as the seed for pseudo-random number generator. Use <int> as the seed for pseudo-random number generator. Best alignments Best alignments Make Bowtie guarantee that reported singleton alignments are best in terms of stratum (i.e. number of mismatches, or mismatches in the seed in the case of -n mode) and in terms of the quality values at the mismatched position(s). bowtie is somewhat slower when --best is specified. Make Bowtie guarantee that reported singleton alignments are best in terms of stratum (i.e. number of mismatches, or mismatches in the seed in the case of -n mode) and in terms of the quality values at the mismatched position(s). bowtie is somewhat slower when --best is specified. All alignments All alignments Report all valid alignments per read or pair. Report all valid alignments per read or pair. Colorspace Colorspace When -C is specified, read sequences are treated as colors. Colors may be encoded either as numbers (0=blue, 1=green, 2=orange, 3=red) or as characters A/C/G/T (A=blue, C=green, G=orange, T=red). When -C is specified, read sequences are treated as colors. Colors may be encoded either as numbers (0=blue, 1=green, 2=orange, 3=red) or as characters A/C/G/T (A=blue, C=green, G=orange, T=red). Align Reads with Bowtie Align Reads with Bowtie Performs alignment of short reads with Bowtie. Performs alignment of short reads with Bowtie. U2::LocalWorkflow::BwaMemWorker Number of threads Number of threads Number of threads (-t). Number of threads (-t). Min seed length Min seed length Path to indexed reference genome (-k). Path to indexed reference genome (-k). Index algorithm Index algorithm Index algorithm (-a). Index algorithm (-a). Band width Band width Band width for banded alignment (-w). Band width for banded alignment (-w). Dropoff Dropoff Off-diagonal X-dropoff (-d). Off-diagonal X-dropoff (-d). Internal seed length Internal seed length Look for internal seeds inside a seed longer than {-k} (-r). Look for internal seeds inside a seed longer than {-k} (-r). Skip seed threshold Skip seed threshold Skip seeds with more than INT occurrences (-c). Skip seeds with more than INT occurrences (-c). Drop chain threshold Drop chain threshold Drop chains shorter than FLOAT fraction of the longest overlapping chain (-D). Drop chains shorter than FLOAT fraction of the longest overlapping chain (-D). Rounds of mate rescues Rounds of mate rescues Perform at most INT rounds of mate rescues for each read (-m). Perform at most INT rounds of mate rescues for each read (-m). Skip mate rescue Skip mate rescue Skip mate rescue (-S). Skip mate rescue (-S). Skip pairing Skip pairing Skip pairing; mate rescue performed unless -S also in use (-P). Skip pairing; mate rescue performed unless -S also in use (-P). Matching score Mismatch penalty Mismatch penalty Score for a sequence match (-A). Score for a sequence match (-A). Penalty for a mismatch (-B). Penalty for a mismatch (-B). Gap open penalty Gap open penalty Gap open penalty (-O). Gap open penalty (-O). Gap extension penalty Gap extension penalty Gap extension penalty; a gap of size k cost {-O} (-E). Gap extension penalty; a gap of size k cost {-O} (-E). Penalty for clipping Penalty for clipping Penalty for clipping (-L). Penalty for clipping (-L). Penalty unpaired Penalty unpaired Penalty for an unpaired read pair (-U). Penalty for an unpaired read pair (-U). Score threshold Score threshold Minimum score to output (-T). Minimum score to output (-T). Align Reads with BWA MEM Align Reads with BWA MEM Performs alignment of short reads with BWA MEM. Performs alignment of short reads with BWA MEM. U2::LocalWorkflow::BwaWorker Use missing prob Use missing prob Use missing prob instead maximum edit distance. Use missing prob instead maximum edit distance. Max #diff Max #diff Max #diff (-n) Max #diff (-n) Missing prob Missing prob Missing prob (-n) Missing prob (-n) Seed length Seed length Seed length (-l). Seed length (-l). Max gap opens Max gap opens Max gap opens (-o). Max gap opens (-o). Index algorithm Index algorithm Index algorithm (-a). Index algorithm (-a). Best hits Best hits Best hits (-R). Best hits (-R). Long-scaled gap penalty for long deletions Long-scaled gap penalty for long deletions Long-scaled gap penalty for long deletions (-L) Long-scaled gap penalty for long deletions (-L) Non iterative mode Non iterative mode Non iterative mode (-N). Non iterative mode (-N). Enable long gaps Enable long gaps Max gap extensions Max gap extensions Max gap extensions (-e) Max gap extensions (-e) Indel offset Indel offset Indel offset (-i) Indel offset (-i) Max long deletions extensions Max long deletions extensions Max long deletions extensions(-d) Max long deletions extensions(-d) Max queue entries Max queue entries Max queue entries (-m) Max queue entries (-m) Barcode length Barcode length Barcode length (-B) Barcode length (-B) Threads Threads Threads (-t) Threads (-t) Max seed differencies Max seed differencies Max seed differencies (-k) Max seed differencies (-k) Mismatch penalty Mismatch penalty Mismatch penalty (-M) Mismatch penalty (-M) Gap open penalty Gap open penalty Gap open penalty (-O). Gap open penalty (-O). Gap extension penalty Gap extension penalty Gap extension penalty; a gap of size k cost (-E). Gap extension penalty; a gap of size k cost (-E). Quolity threshold Quality threshold Quolity threshold (-q). Quality threshold (-q). Align Reads with BWA Align Reads with BWA Performs alignment of short reads with BWA. Performs alignment of short reads with BWA. U2::LocalWorkflow::CAP3Prompter from %1 from %1 U2::LocalWorkflow::CAP3Worker Input sequences Input sequences DNA sequences that need to be assembled DNA sequences that need to be assembled Input URL(s) Input URL(s) URL(s) of input file(s) in FASTA format with DNA sequences that need to be assembled URL(s) of input file(s) in FASTA format with DNA sequences that need to be assembled Assembly Sequences with CAP3 Assembly Sequences with CAP3 Output file Output file Write assembly results to this output file in ACE format. Write assembly results to this output file in ACE format. Quality cutoff for clipping Quality cutoff for clipping Base quality cutoff for clipping (-c) Base quality cutoff for clipping (-c) Clipping range Clipping range One of the parameters to control clipping of a poor end region of a read (-y)If there are quality values, CAP3 computes two positions qualpos5 and qualpos3 of read f such that the region of read f from position qualpos5 to position qualpos3 consists mostly of quality values greater than Quality cutoff for clipping. If there are no quality values, then qualpos5 is set to 1 and qualpos3 is set the length of read f. The range for the left clipping position of read f is from 1 to qualpos5 + Clipping range. The range for the right clipping position of read f is from qualpos3 - Clipping range to the end of read f. One of the parameters to control clipping of a poor end region of a read (-y)If there are quality values, CAP3 computes two positions qualpos5 and qualpos3 of read f such that the region of read f from position qualpos5 to position qualpos3 consists mostly of quality values greater than Quality cutoff for clipping. If there are no quality values, then qualpos5 is set to 1 and qualpos3 is set the length of read f. The range for the left clipping position of read f is from 1 to qualpos5 + Clipping range. The range for the right clipping position of read f is from qualpos3 - Clipping range to the end of read f. Quality cutoff for differences Quality cutoff for differences Base quality cutoff for differences (-b) Base quality cutoff for differences (-b) Maximum difference score Maximum difference score Max qscore sum at differences (-d)If an overlap contains lots of differences at bases of high quality, then the overlap is removed.The difference score is calculated as follows. If the overlap contains a difference at bases of quality values q1 and q2, then the score at the difference is max(0, min(q1, q2) - b), where b is Quality cutoff for differences. The difference score of an overlap is the sum of scores at each difference. Max qscore sum at differences (-d)If an overlap contains lots of differences at bases of high quality, then the overlap is removed.The difference score is calculated as follows. If the overlap contains a difference at bases of quality values q1 and q2, then the score at the difference is max(0, min(q1, q2) - b), where b is Quality cutoff for differences. The difference score of an overlap is the sum of scores at each difference. Match score factor Match score factor Match score factor (-m) is one of the parameters that affects similarity score of an overlap. See Overlap similarity score cutoff description for details. Match score factor (-m) is one of the parameters that affects similarity score of an overlap. See Overlap similarity score cutoff description for details. Mismatch score factor Mismatch score factor Mismatch score factor (-n) is one of the parameters that affects similarity score of an overlap. See Overlap similarity score cutoff description for details. Mismatch score factor (-n) is one of the parameters that affects similarity score of an overlap. See Overlap similarity score cutoff description for details. Gap penalty factor Gap penalty factor Gap penalty factor (-g) is one of the parameters that affects similarity score of an overlap. See Overlap similarity score cutoff description for details. Gap penalty factor (-g) is one of the parameters that affects similarity score of an overlap. See Overlap similarity score cutoff description for details. Overlap similarity score cutoff Overlap similarity score cutoff If the similarity score of an overlap is less than the overlap similarity score cutoff (-s), then the overlap is removed.The similarity score of an overlapping alignment is defined using base quality values as follows.A match at bases of quality values q1 and q2 is given a score of m * min(q1,q2), where m is Match score factor.A mismatch at bases of quality values q1 and q2 is given a score of n * min(q1,q2), where n is Mismatch score factor.A base of quality value q1 in a gap is given a score of -g * min(q1,q2), where q2 is the quality value of the base in the other sequence right before the gap and g is Gap penalty factor.The score of a gap is the sum of scores of each base in the gap minus a gap open penalty.The similarity score of an overlapping alignment is the sum of scores of each match, each mismatch, and each gap. If the similarity score of an overlap is less than the overlap similarity score cutoff (-s), then the overlap is removed.The similarity score of an overlapping alignment is defined using base quality values as follows.A match at bases of quality values q1 and q2 is given a score of m * min(q1,q2), where m is Match score factor.A mismatch at bases of quality values q1 and q2 is given a score of n * min(q1,q2), where n is Mismatch score factor.A base of quality value q1 in a gap is given a score of -g * min(q1,q2), where q2 is the quality value of the base in the other sequence right before the gap and g is Gap penalty factor.The score of a gap is the sum of scores of each base in the gap minus a gap open penalty.The similarity score of an overlapping alignment is the sum of scores of each match, each mismatch, and each gap. Overlap length cutoff Overlap length cutoff An overlap is taken into account only if the length of the overlap in bp is no less than the specified value (parameter -o of CAP3). An overlap is taken into account only if the length of the overlap in bp is no less than the specified value (parameter -o of CAP3). Overlap percent identity cutoff Overlap percent identity cutoff An overlap is taken into account only if the percent identity of the overlap is no less than the specified value (parameter -p of CAP3). An overlap is taken into account only if the percent identity of the overlap is no less than the specified value (parameter -p of CAP3). Max number of word matches Max number of word matches This parameter allows one to trade off the efficiency of the program for its accuracy (parameter -t of CAP3).For a read f, CAP3 computes overlaps between read f and other reads by considering short word matches between read f and other reads. A word match is examined to see if it can be extended into a long overlap. If read f has overlaps with many other reads, then read f has many short word matches with many other reads.This parameter gives an upper limit, for any word, on the number of word matches between read f and other reads that are considered by CAP3.Using a large value for this parameter allows CAP3 to consider more word matches between read f and other reads, which can find more overlaps for read f, but slows down the program.Using a small value for this parameter has the opposite effect. This parameter allows one to trade off the efficiency of the program for its accuracy (parameter -t of CAP3).For a read f, CAP3 computes overlaps between read f and other reads by considering short word matches between read f and other reads. A word match is examined to see if it can be extended into a long overlap. If read f has overlaps with many other reads, then read f has many short word matches with many other reads.This parameter gives an upper limit, for any word, on the number of word matches between read f and other reads that are considered by CAP3.Using a large value for this parameter allows CAP3 to consider more word matches between read f and other reads, which can find more overlaps for read f, but slows down the program.Using a small value for this parameter has the opposite effect. Band expansion size Band expansion size CAP3 determines a minimum band of diagonals for an overlapping alignment between two sequence reads. The band is expanded by a number of bases specified by this value (parameter -a of CAP3). CAP3 determines a minimum band of diagonals for an overlapping alignment between two sequence reads. The band is expanded by a number of bases specified by this value (parameter -a of CAP3). Max gap length in an overlap Max gap length in an overlap The maximum length of gaps allowed in any overlap (-f)I.e. overlaps with longer gaps are rejected.Note that a small value for this parameter may cause the program to remove true overlaps and to produce incorrect results.The parameter may be used to split reads from alternative splicing forms into separate contigs. The maximum length of gaps allowed in any overlap (-f)I.e. overlaps with longer gaps are rejected.Note that a small value for this parameter may cause the program to remove true overlaps and to produce incorrect results.The parameter may be used to split reads from alternative splicing forms into separate contigs. Assembly reverse reads Assembly reverse reads Specifies whether to consider reads in reverse orientation for assembly (originally, parameter -r of CAP3). Specifies whether to consider reads in reverse orientation for assembly (originally, parameter -r of CAP3). CAP3 tool path CAP3 tool path The path to the CAP3 external tool in UGENE. The path to the CAP3 external tool in UGENE. Temporary folder Temporary folder The folder for temporary files. The folder for temporary files. Aligns long DNA reads from %1 with CAP3. Aligns long DNA reads from %1 with CAP3. U2::LocalWorkflow::CEASReportPrompter Creates summary statistics on ChIP enrichment and saves it to %1. Creates summary statistics on ChIP enrichment and saves it to %1. U2::LocalWorkflow::CEASReportWorker Peak regions Peak regions Peak regions. Peak regions. Enrichment signal Enrichment signal Enrichment signal. Enrichment signal. CEAS data CEAS data Peak regions and enrichment signal profile for generating CEAS report. Peak regions and enrichment signal profile for generating CEAS report. Output report file Output report file Path to the report output file. Result for CEAS analysis. Path to the report output file. Result for CEAS analysis. Output annotations file Output annotations file Name of tab-delimited output text file, containing a row of annotations for every RefSeq gene. (file is not generated if no peak location data is supplied). Name of tab-delimited output text file, containing a row of annotations for every RefSeq gene. (file is not generated if no peak location data is supplied). Gene annotations table Gene annotations table Path to gene annotation table (e.g. a refGene table in sqlite3 db format (--gt). Path to gene annotation table (e.g. a refGene table in sqlite3 db format (--gt). Span size Span size Span from TSS and TTS in the gene-centered annotation (base pairs). ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates in promoter and downstream (--span). Span from TSS and TTS in the gene-centered annotation (base pairs). ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates in promoter and downstream (--span). Wiggle profiling resolution Wiggle profiling resolution Wiggle profiling resolution. WARNING: Value smaller than the wig interval (resolution) may cause aliasing error (--pf-res). Wiggle profiling resolution. WARNING: Value smaller than the wig interval (resolution) may cause aliasing error (--pf-res). Promoter/downstream interval Promoter/downstream interval Promoter/downstream intervals for ChIP region annotation are three values or a single value can be given. If a single value is given, it will be segmented into three equal fractions (e.g. 3000 is equivalent to 1000,2000,3000) (--rel-dist). Promoter/downstream intervals for ChIP region annotation are three values or a single value can be given. If a single value is given, it will be segmented into three equal fractions (e.g. 3000 is equivalent to 1000,2000,3000) (--rel-dist). BiPromoter ranges BiPromoter ranges Bidirectional-promoter sizes for ChIP region annotation. It's two values or a single value can be given. If a single value is given, it will be segmented into two equal fractions (e.g. 5000 is equivalent to 2500,5000) (--bisizes). Bidirectional-promoter sizes for ChIP region annotation. It's two values or a single value can be given. If a single value is given, it will be segmented into two equal fractions (e.g. 5000 is equivalent to 2500,5000) (--bisizes). Relative distance Relative distance Relative distance to TSS/TTS in WIGGLE file. profiling. (--rel-dist) Relative distance to TSS/TTS in WIGGLE file. profiling. (--rel-dist) Gene group files Gene group files Gene groups of particular interest in wig profiling. Each gene group file must have gene names in the 1st column. The file names are separated by commas (--gn-groups). Gene groups of particular interest in wig profiling. Each gene group file must have gene names in the 1st column. The file names are separated by commas (--gn-groups). Gene group names Gene group names Set this parameter empty for using default values. The names of the gene groups from "Gene group files" parameter. These names appear in the legends of the wig profiling plots. Values range: comma-separated list of strings. Default value: 'Group 1, Group 2,...Group n' (--gn-group-names). Set this parameter empty for using default values. The names of the gene groups from "Gene group files" parameter. These names appear in the legends of the wig profiling plots. Values range: comma-separated list of strings. Default value: 'Group 1, Group 2,...Group n' (--gn-group-names). Report file Report file Annotations file Annotations file Create CEAS Report Create CEAS Report Provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study. Provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study. U2::LocalWorkflow::ClustalOPrompter from %1 from %1 Aligns each MSA supplied %1 with "ClustalO". Aligns each MSA supplied %1 with "ClustalO". U2::LocalWorkflow::ClustalOWorker Input MSA Input MSA Input MSA to process. Input MSA to process. ClustalO result MSA ClustalO result MSA The result of the ClustalO alignment. The result of the ClustalO alignment. Number of iterations Number of iterations Number of (combined guide-tree/HMM) iterations. Number of (combined guide-tree/HMM) iterations. Number of guidetree iterations Number of guidetree iterations Maximum number guidetree iterations. Maximum number guidetree iterations. Number of HMM iterations Number of HMM iterations Maximum number of HMM iterations. Maximum number of HMM iterations. Set auto options Set auto options Set options automatically (might overwrite some of your options). Set options automatically (might overwrite some of your options). Tool path Tool path Path to the ClustalO tool.The default path can be set in the UGENE application settings. Path to the ClustalO tool.The default path can be set in the UGENE application settings. Temporary folder Temporary folder Folder to store temporary files. Folder to store temporary files. Align with ClustalO Align with ClustalO Aligns multiple sequence alignments (MSAs) supplied with ClustalO.ClustalO is a general purpose multiple sequence alignment program for proteins.Visit <a href="http://www.clustal.org/omega">http://www.clustal.org/omega</a> to learn more about it. Aligns multiple sequence alignments (MSAs) supplied with ClustalO.ClustalO is a general purpose multiple sequence alignment program for proteins.Visit <a href="http://www.clustal.org/omega">http://www.clustal.org/omega</a> to learn more about it. An empty MSA '%1' has been supplied to ClustalO. An empty MSA '%1' has been supplied to ClustalO. Aligned %1 with ClustalO Aligned %1 with ClustalO U2::LocalWorkflow::ClustalWPrompter from %1 from %1 Aligns each MSA supplied %1 with "ClustalW". Aligns each MSA supplied %1 with "ClustalW". U2::LocalWorkflow::ClustalWWorker Input MSA Input MSA Input MSA to process. Input MSA to process. ClustalW result MSA ClustalW result MSA The result of the ClustalW alignment. The result of the ClustalW alignment. Gap open penalty Gap open penalty The penalty for opening a gap. The penalty for opening a gap. Gap extension penalty Gap extension penalty The penalty for extending a gap. The penalty for extending a gap. Gap distance Gap distance The gap separation penalty. Tries to decrease the chances of gaps being too close to each other. The gap separation penalty. Tries to decrease the chances of gaps being too close to each other. End gaps End gaps The penalty for closing a gap. The penalty for closing a gap. Residue-specific gaps off Residue-specific gaps off Residue-specific penalties are amino specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment. Residue-specific penalties are amino specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment. Hydrophilic gaps off Hydrophilic gaps off Hydrophilic gap penalties are used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids. Hydrophilic gap penalties are used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids. Iteration type Iteration type Alignment improvement iteration type. Can take values: <ul> <li>None - No iteration;</li> <li>Tree - Iteration at each step of alignment process;</li> <li>Alignment - Iteration only on final alignment.</li> </ul> Alignment improvement iteration type. Can take values: <ul> <li>None - No iteration;</li> <li>Tree - Iteration at each step of alignment process;</li> <li>Alignment - Iteration only on final alignment.</li> </ul> Number of iterations Number of iterations The maximum number of iterations to perform. The maximum number of iterations to perform. Weight matrix Weight matrix Tool path Tool path Path to the ClustalW tool.The default path can be set in the UGENE application settings. Path to the ClustalW tool.The default path can be set in the UGENE application settings. Folder to store temporary files. Folder to store temporary files. Aligns multiple sequence alignments (MSAs) supplied with ClustalW.ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.Visit <a href="http://www.clustal.org/">http://www.clustal.org/</a> to learn more about it. Aligns multiple sequence alignments (MSAs) supplied with ClustalW.ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.Visit <a href="http://www.clustal.org/">http://www.clustal.org/</a> to learn more about it. An empty MSA '%1' has been supplied to ClustalW. An empty MSA '%1' has been supplied to ClustalW. Temporary folder Temporary folder For proteins it is a scoring table which describes the similarity of each amino acid to each other and can take values: <ul> <li>BLOSUM - Appear to be the best available for carrying out database similarity (homology searches). <li>PAM - Have been extremely widely used since the late '70s. <li>Gonnet - Derived using almost the same procedure as the PAM bit are much more up to date. <li>ID - Identitical matrix gives a score of 1.0 to two identical amino acids and a score of zero otherwise. </ul> For DNA it is the scores assigned to matches and mismatches. The values available are: <ul> <li>IUB - The default scoring matrix used by BESTFIT for the comparison of nucleic acid sequences. All matches score 1.9; all mismatches for IUB symbols score 0. <li>ClustalW - The previous system used by Clustal W, in which matches score 1.0 and mismatches score 0. All matches for IUB symbols also score 0. </ul> For proteins it is a scoring table which describes the similarity of each amino acid to each other and can take values: <ul> <li>BLOSUM - Appear to be the best available for carrying out database similarity (homology searches). <li>PAM - Have been extremely widely used since the late '70s. <li>Gonnet - Derived using almost the same procedure as the PAM bit are much more up to date. <li>ID - Identitical matrix gives a score of 1.0 to two identical amino acids and a score of zero otherwise. </ul> For DNA it is the scores assigned to matches and mismatches. The values available are: <ul> <li>IUB - The default scoring matrix used by BESTFIT for the comparison of nucleic acid sequences. All matches score 1.9; all mismatches for IUB symbols score 0. <li>ClustalW - The previous system used by Clustal W, in which matches score 1.0 and mismatches score 0. All matches for IUB symbols also score 0. </ul> Align with ClustalW Align with ClustalW Aligned %1 with ClustalW Aligned %1 with ClustalW U2::LocalWorkflow::ConductGOPrompter unset unset Uses annotations from %1 as gene list to conduct GO. Uses annotations from %1 as gene list to conduct GO. Outputs all result files to %1 folder Outputs all result files to %1 folder U2::LocalWorkflow::ConductGOWorker Target genes Target genes Gene list to identify over represented GO terms. Gene list to identify over represented GO terms. URL to file with genes to identify over represented GO terms. Conduct GO data Conduct GO data Output folder Output folder The folder to store Conduct GO results. The folder to store Conduct GO results. Title Title Title is used to name the output files - so make it meaningful. Title is used to name the output files - so make it meaningful. Gene Universe Gene Universe Select a gene universe. Select a gene universe. Conduct GO Conduct GO Given a list of genes, using Bioconductor (GO, GOstats) and DAVID at NIH. Given a list of genes, using Bioconductor (GO, GOstats) and DAVID at NIH. U2::LocalWorkflow::ConservationPlotPrompter unset unset Uses annotations from %1 as peak regions for conservation plot. Uses annotations from %1 as peak regions for conservation plot. Conservations scores from %1. Conservations scores from %1. Outputs the result to %1 Outputs the result to %1 U2::LocalWorkflow::ConservationPlotWorker Input regions Input regions Regions (centered at peak summits for better performance). Regions (centered at peak summits for better performance). conservation_plot data conservation_plot data Regions to plot the PhastCons scores profiles. Regions to plot the PhastCons scores profiles. Output file Output file File to store phastcons results (BMP). File to store phastcons results (BMP). Title Title Title of the figure (--title). Title of the figure (--title). Label Label Label of data in the figure (--bed-label). Label of data in the figure (--bed-label). Assembly version Assembly version The folder to store phastcons scores (--phasdb). The folder to store phastcons scores (--phasdb). Window width Window width Window width centered at middle of regions (-w). Window width centered at middle of regions (-w). Height Height Height of plot (--height). Height of plot (--height). Width Width Width of plot (--width). Width of plot (--width). Conservation plot file Conservation plot file Build Conservation Plot Build Conservation Plot Plots the PhastCons scores profiles. Plots the PhastCons scores profiles. U2::LocalWorkflow::CuffdiffWorker Test for Diff. Expression with Cuffdiff Test for Diff. Expression with Cuffdiff Cuffdiff takes a transcript file as input, along with two or more fragment alignments (e.g. in SAM format) for two or more samples. It produces a number of output files that contain test results for changes in expression at the level of transcripts, primary transcripts, and genes. It also tracks changes in the relative abundance of transcripts sharing a common transcription start site, and in the relative abundances of the primary transcripts of each gene. Tracking the former allows one to see changes in splicing, and the latter lets one see changes in relative promoter use within a gene. Cuffdiff takes a transcript file as input, along with two or more fragment alignments (e.g. in SAM format) for two or more samples. It produces a number of output files that contain test results for changes in expression at the level of transcripts, primary transcripts, and genes. It also tracks changes in the relative abundance of transcripts sharing a common transcription start site, and in the relative abundances of the primary transcripts of each gene. Tracking the former allows one to see changes in splicing, and the latter lets one see changes in relative promoter use within a gene. Output folder Output folder The base name of output folder. It could be modified with a suffix. The base name of output folder. It could be modified with a suffix. Time series analysis Time series analysis If set to True, instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order. If set to True, instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order. Upper quartile norm Upper quartile norm If set to True, normalizes by the upper quartile of the number of fragments mapping to individual loci instead of the total number of sequenced fragments. This can improve robustness of differential expression calls for less abundant genes and transcripts. If set to True, normalizes by the upper quartile of the number of fragments mapping to individual loci instead of the total number of sequenced fragments. This can improve robustness of differential expression calls for less abundant genes and transcripts. Hits norm Hits norm Instructs how to count all fragments. Total specifies to count all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator. Compatible specifies to use only compatible fragments. Selecting Compatible is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. Instructs how to count all fragments. Total specifies to count all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator. Compatible specifies to use only compatible fragments. Selecting Compatible is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. Frag bias correct Frag bias correct Providing the sequences your reads were mapped to instructs Cuffdiff to run bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates. Providing the sequences your reads were mapped to instructs Cuffdiff to run bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates. Multi read correct Multi read correct Do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome. Do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome. Library type Library type Specifies RNA-Seq protocol. Specifies RNA-Seq protocol. Mask file Mask file Ignore all reads that could have come from transcripts in this file. It is recommended to include any annotated rRNA, mitochondrial transcripts other abundant transcripts you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment methods and rRNA depletion kits, masking these transcripts often improves the overall robustness of transcript abundance estimates. Ignore all reads that could have come from transcripts in this file. It is recommended to include any annotated rRNA, mitochondrial transcripts other abundant transcripts you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment methods and rRNA depletion kits, masking these transcripts often improves the overall robustness of transcript abundance estimates. Ignore all reads that could have come from transcripts in this file. It is recommended to include any annotated rRNA, mitochondrial transcripts or other abundant transcripts you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment methods and rRNA depletion kits, masking these transcripts often improves the overall robustness of transcript abundance estimates. Min alignment count Min alignment count The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. FDR FDR The allowed false discovery rate used in testing. The allowed false discovery rate used in testing. Max MLE iterations Max MLE iterations Sets the number of iterations allowed during maximum likelihood estimation of abundances. Sets the number of iterations allowed during maximum likelihood estimation of abundances. Emit count tables Emit count tables Include information about the fragment counts, fragment count variances, and fitted variance model into the report. Include information about the fragment counts, fragment count variances, and fitted variance model into the report. Cuffdiff tool path Cuffdiff tool path The path to the Cuffdiff external tool in UGENE. The path to the Cuffdiff external tool in UGENE. Temporary folder Temporary folder The folder for temporary files. The folder for temporary files. Assembly Assembly RNA-Seq reads assemblies RNA-Seq reads assemblies Annotations Annotations Transcript annotations Transcript annotations Sample Sample Sample name of assembly file Sample name of assembly file Total Compatible Searches for significant changes in transcript expression, splicing and promoter use. Searches for significant changes in transcript expression, splicing and promoter use. U2::LocalWorkflow::CufflinksWorker Input reads Input reads Input RNA-Seq read alignments. Input RNA-Seq read alignments. Output annotations Output annotations Assembled isoforms, estimated isoform-level expression values, and estimated gene-level expression values, produced by Cufflinks. Assembled isoforms, estimated isoform-level expression values, and estimated gene-level expression values, produced by Cufflinks. Isoform-level expression values Isoform-level expression values A set of annotated regions A set of annotated regions Assembly Transcripts with Cufflinks Assembly Transcripts with Cufflinks Cufflinks accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. Cufflinks accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. Output folder Output folder The base name of output folder. It could be modified with a suffix. The base name of output folder. It could be modified with a suffix. Reference annotation Reference annotation Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. Cufflinks will not assemble novel transcripts and the program will ignore alignments not structurally compatible with any reference transcript. Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. Cufflinks will not assemble novel transcripts and the program will ignore alignments not structurally compatible with any reference transcript. RABT annotation RABT annotation Tells Cufflinks to use the supplied reference annotation to guide Reference Annotation Based Transcript (RABT) assembly. Reference transcripts will be tiled with faux-reads to provide additional information in assembly. Output will include all reference transcripts as well as any novel genes and isoforms that are assembled. Tells Cufflinks to use the supplied reference annotation to guide Reference Annotation Based Transcript (RABT) assembly. Reference transcripts will be tiled with faux-reads to provide additional information in assembly. Output will include all reference transcripts as well as any novel genes and isoforms that are assembled. Library type Library type Specifies RNA-Seq protocol. Specifies RNA-Seq protocol. Mask file Mask file Ignore all reads that could have come from transcripts in this file. It is recommended to include any annotated rRNA, mitochondrial transcripts or other abundant transcripts you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment methods and rRNA depletion kits, masking these transcripts often improves the overall robustness of transcript abundance estimates. Ignore all reads that could have come from transcripts in this file. It is recommended to include any annotated rRNA, mitochondrial transcripts other abundant transcripts you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment methods and rRNA depletion kits, masking these transcripts often improves the overall robustness of transcript abundance estimates. Ignore all reads that could have come from transcripts in this file. It is recommended to include any annotated rRNA, mitochondrial transcripts other abundant transcripts you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment methods and rRNA depletion kits, masking these transcripts often improves the overall robustness of transcript abundance estimates. Multi-read correct Multi-read correct Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome. Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome. Min isoform fraction Min isoform fraction After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. Frag bias correct Frag bias correct Providing Cufflinks with a multifasta file via this option instructs it to run the bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates. Providing Cufflinks with a multifasta file via this option instructs it to run the bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates. Pre-mRNA fraction Pre-mRNA fraction Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. Cufflinks tool path Cufflinks tool path The path to the Cufflinks external tool in UGENE. The path to the Cufflinks external tool in UGENE. Temporary folder Temporary folder The folder for temporary files. The folder for temporary files. Incorrect value of the library type parameter for Cufflinks! Incorrect value of the library type parameter for Cufflinks! U2::LocalWorkflow::CuffmergeWorker Merge Assemblies with Cuffmerge Merge Assemblies with Cuffmerge Cuffmerge merges together several assemblies. It also handles running Cuffcompare for you, and automatically filters a number of transfrags that are probably artifacts. If you have a reference file available, you can provide it to Cuffmerge in order to gracefully merge input (e.g. novel) isoforms and known isoforms and maximize overall assembly quality. Cuffmerge merges together several assemblies. It also handles running Cuffcompare for you, and automatically filters a number of transfrags that are probably artifacts. If you have a reference file available, you can provide it to Cuffmerge in order to gracefully merge input (e.g. novel) isoforms and known isoforms and maximize overall assembly quality. Output folder Output folder The base name of output folder. It could be modified with a suffix. The base name of output folder. It could be modified with a suffix. Reference annotation Reference annotation Merge the input assemblies together with this reference annotation. Merge the input assemblies together with this reference annotation. Reference sequence Reference sequence The genomic DNA sequences for the reference. It is used to assist in classifying transfrags and excluding artifacts (e.g. repeats). For example, transcripts consisting mostly of lower-case bases are classified as repeats. The genomic DNA sequences for the reference. It is used to assist in classifying transfrags and excluding artifacts (e.g. repeats). For example, transcripts consisting mostly of lower-case bases are classified as repeats. Minimum isoform fraction Minimum isoform fraction Discard isoforms with abundance below this. Discard isoforms with abundance below this. Cuffcompare tool path Cuffcompare tool path The path to the Cuffcompare external tool in UGENE. The path to the Cuffcompare external tool in UGENE. Cuffmerge tool path Cuffmerge tool path The path to the Cuffmerge external tool in UGENE. The path to the Cuffmerge external tool in UGENE. Temporary folder Temporary folder The folder for temporary files. The folder for temporary files. Set of annotations Set of annotations Annotations for merging Annotations for merging Merged annotations Merged annotations Merges together supplied assemblies. Merges together supplied assemblies. U2::LocalWorkflow::CutAdaptFastqPrompter unset unset from %1 from %1 Removes adapter sequences %1. Removes adapter sequences %1. U2::LocalWorkflow::CutAdaptFastqTask Can not copy the result file to: %1 Can not copy the result file to: %1 Unknown file format: Unknown file format: U2::LocalWorkflow::CutAdaptFastqWorker Cut Adapter Cut Adapter Removes adapter sequences Removes adapter sequences Input File Input File Set of FASTQ reads files Set of FASTQ reads files Output File Output File Output FASTQ file(s) Output FASTQ file(s) Output folder Output folder Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Custom folder Custom folder Select the custom output folder. Select the custom output folder. Output file name Output file name A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. FASTA file with 3' adapters A FASTA file with one or multiple sequences of adapter that were ligated to the 3' end. The adapter itself and anything that follows is trimmed. If the adapter sequence ends with the '$' character, the adapter is anchored to the end of the read and only found if it is a suffix of the read. FASTA file with 5' adapters FASTA file with adapters FASTA file with adapters A FASTA file with one or multiple sequences of adapter that were ligated to the 3' end. The adapter itself and anything that follows is trimmed. If the adapter sequence ends with the '$ character, the adapter is anchored to the end of the read and only found if it is a suffix of the read. A FASTA file with one or multiple sequences of adapter that were ligated to the 3' end. The adapter itself and anything that follows is trimmed. If the adapter sequence ends with the '$ character, the adapter is anchored to the end of the read and only found if it is a suffix of the read. FASTA file with reverse adapters FASTA file with reverse adapters A FASTA file with one or multiple sequences of adapters that were ligated to the 5' end. If the adapter sequence starts with the character '^', the adapter is 'anchored'. An anchored adapter must appear in its entirety at the 5' end of the read (it is a prefix of the read). A non-anchored adapter may appear partially at the 5' end, or it may occur within the read. If it is found within a read, the sequence preceding the adapter is also trimmed. In all cases, the adapter itself is trimmed. A FASTA file with one or multiple sequences of adapters that were ligated to the 5' end. If the adapter sequence starts with the character '^', the adapter is 'anchored'. An anchored adapter must appear in its entirety at the 5' end of the read (it is a prefix of the read). A non-anchored adapter may appear partially at the 5' end, or it may occur within the read. If it is found within a read, the sequence preceding the adapter is also trimmed. In all cases, the adapter itself is trimmed. FASTA file with 5' and 3' adapters FASTA file with 5' and 3' adapters A FASTA file with one or multiple sequences of adapters that were ligated to the 5' end or 3' end. A FASTA file with one or multiple sequences of adapters that were ligated to the 5' end or 3' end. Input file Input file Workflow Workflow Custom Custom U2::LocalWorkflow::FastQCPrompter unset unset from %1 from %1 Builds FastQC report for file(s) %1. Builds FastQC report for file(s) %1. U2::LocalWorkflow::FastQCWorker FastQC Quality Control FastQC Quality Control Builds quality control reports. Builds quality control reports. Short reads Short reads Short read data Short read data Output folder Output folder Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Custom folder Custom folder Select the custom output folder. Select the custom output folder. List of adapters List of adapters Specifies a non-default file which contains the list of adapter sequences which will be explicity searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored. Specifies a non-default file which contains the list of adapter sequences which will be explicity searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored. List of contaminants List of contaminants Specifies a non-default file which contains the list of contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored. Specifies a non-default file which contains the list of contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored. Input file Input file Workflow Workflow Custom Custom U2::LocalWorkflow::GenomecovPrompter unset unset from %1 from %1 %1 from %2 with bedtool genomecov. %1 from %2 with bedtool genomecov. U2::LocalWorkflow::GenomecovTask Unknown file format: Unknown file format: U2::LocalWorkflow::GenomecovWorker Genome Coverage Genome Coverage Calculates genome coverage using bedtools genomecov. Calculates genome coverage using bedtools genomecov. Input File Input File Set of files to NGS slop Set of files to NGS slop Output File Output File Output file Output file Output folder Output folder Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Custom folder Custom folder Select the custom output folder. Select the custom output folder. Output file name Output file name A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. Genome Genome In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. The format of the file is: <chromName><TAB><chromSize>. (-g) In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. The format of the file is: <chromName><TAB><chromSize>. (-g) Report mode Report mode %1 (%2) - %3 %4 (%5) - %6 %7 (%8) - %9 %10 (%11) - %12 %13 (%14) - %15 %1 (%2) - %3 %4 (%5) - %6 %7 (%8) - %9 %10 (%11) - %12 %13 (%14) - %15 Split Split Treat âsplitâ BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR âNâ and âDâ operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). (-split) Treat BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR and operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). (-split) Strand Strand Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6). (-strand) Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6). (-strand) 5 prime 5 prime Calculate coverage of 5â positions (instead of entire interval). (-5) Calculate coverage of 5' positions (instead of entire interval). (-5) 3 prime 3 prime Calculate coverage of 3â positions (instead of entire interval). (-3) Calculate coverage of 3' positions (instead of entire interval). (-3) Max Max Combine all positions with a depth >= max into a single bin in the histogram. (-max) Combine all positions with a depth >= max into a single bin in the histogram. (-max) Scale Scale Scale the coverage by a constant factor.Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). Default is 1.0; i.e., unscaled. (-scale) Scale the coverage by a constant factor.Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). Default is 1.0; i.e., unscaled. (-scale) Trackline Trackline Adds a UCSC/Genome-Browser track line definition in the first line of the output. (-trackline) Adds a UCSC/Genome-Browser track line definition in the first line of the output. (-trackline) Trackopts Trackopts Writes additional track line definition parameters in the first line. (-trackopts) Writes additional track line definition parameters in the first line. (-trackopts) Custom Custom Input file Input file Treat “split” BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR “N” and “D” operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). (-split) Calculate coverage of 5’ positions (instead of entire interval). (-5) Calculate coverage of 3’ positions (instead of entire interval). (-3) Workflow Workflow U2::LocalWorkflow::GffreadPrompter Extract transcript sequences from the genomic sequence from %1 using transcripts from %2 and save them to the file %3. Extract transcript sequences from the genomic sequence from %1 using transcripts from %2 and save them to the file %3. U2::LocalWorkflow::HmmerBuildPrompter For each MSA from %1, %1 builds a HMMER profile. U2::LocalWorkflow::HmmerBuildWorker Input MSA Input MSA Input multiple sequence alignment for building statistical model. HMM3 profile Produced HMM3 profile URL Random seed Random seed Random generator seed. 0 - means that one-time arbitrary seed will be used. HMM3 Build Builds a HMM3 profile from a multiple sequence alignment.The HMM3 profile is a statistical model which captures position-specific information about how conserved each column of the alignment is, and which residues are likely. HMMER3 Tools Built HMMER profile U2::LocalWorkflow::HmmerSearchPrompter For each sequence from %1, using all profiles provided by %1, %1 search HMMER signals %2. Output the list of found regions annotated as %4. U2::LocalWorkflow::HmmerSearchWorker Filter by Parameter to filter results by. HMMER profile HMMER profile(s) URL(s) to search with. Input sequence Input sequence An input sequence (nucleotide or protein) to search in. HMMER annotations Annotations marking found similar sequence regions. Result annotation A name of the result annotations. Seed Seed Random generator seed. 0 - means that one-time arbitrary seed will be used. Filter by high E-value Report domains with e-value less than. Filter by low score Report domains with score greater than. HMM3 Search Searches each input sequence for significantly similar sequence matches to all specified HMM profiles. In case several profiles were supplied, searches with all profiles one by one and outputs united set of annotations for each sequence. HMMER3 Tools Value for attribute name is empty, default name used Find HMMER signals in %1 Bad sequence supplied to input: %1 Found %1 HMMER signals U2::LocalWorkflow::MACSPrompter unset unset Uses %1 as treatment Uses %1 as treatment and %1 as control and %1 as control to call peaks. to call peaks. Outputs all files to %1 folder Outputs all files to %1 folder and pileup with %1 span and pileup with %1 span U2::LocalWorkflow::MACSWorker Bad model fold region: %1. Default region is used Bad model fold region: %1. Default region is used unrecognized parsing error Input control and treatment annotations are the same Input control and treatment annotations are the same Treatment features Treatment features ChIP-seq treatment features. ChIP-seq treatment features. Control features Control features Control features (Optional). Control features (Optional). MACS data MACS data ChIP-seq treatment features and control features (optional) to call peaks with MACS. ChIP-seq treatment features and control features (optional) to call peaks with MACS. Peak regions Peak regions Peak locations. Typically used in gene association study like CEAS, or correlation calculation. Peak locations. Typically used in gene association study like CEAS, or correlation calculation. Peak summits Peak summits Peak summits locations for every peaks. Typically used in DNA motif analysis or conservation check. Peak summits locations for every peaks. Typically used in DNA motif analysis or conservation check. Treatment fragments pileup (wiggle) Treatment fragments pileup (wiggle) Wiggle format files which can be imported to UCSC genome browser/GMOD/Affy IGB. Wiggle format files which can be imported to UCSC genome browser/GMOD/Affy IGB. MACS output data MACS output data ChIP-seq peaks and summits. Pileup data (optional) ChIP-seq peaks and summits. Pileup data (optional) Output folder Output folder Folder to save MACS output files. Folder to save MACS output files. Name Name The name string of the experiment. MACS will use this string NAME to create output files like 'NAME_peaks.xls', 'NAME_negative_peaks.xls', 'NAME_peaks.bed', 'NAME_summits.bed', 'NAME_model.r' and so on. So please avoid any confliction between these filenames and your existing files (--name). The name string of the experiment. MACS will use this string NAME to create output files like 'NAME_peaks.xls', 'NAME_negative_peaks.xls', 'NAME_peaks.bed', 'NAME_summits.bed', 'NAME_model.r' and so on. So please avoid any confliction between these filenames and your existing files (--name). Wiggle output Wiggle output If this flag is on, MACS will store the fragment pileup in wiggle format for the whole genome data instead of for every chromosomes (--wig) (--single-profile). If this flag is on, MACS will store the fragment pileup in wiggle format for the whole genome data instead of for every chromosomes (--wig) (--single-profile). Wiggle space Wiggle space By default, the resolution for saving wiggle files is 10 bps,i.e., MACS will save the raw tag count every 10 bps. You can change it along with '--wig' option (--space). By default, the resolution for saving wiggle files is 10 bps,i.e., MACS will save the raw tag count every 10 bps. You can change it along with '--wig' option (--space). Genome size (Mbp) Genome size (Mbp) Homo sapience - 2700 Mbp Mus musculus - 1870 Mbp Caenorhabditis elegans - 90 Mbp Drosophila melanogaster - 120 Mbp It's the mappable genome size or effective genome size which is defined as the genome size which can be sequenced. Because of the repetitive features on the chromosomes, the actual mappable genome size will be smaller than the original size, about 90% or 70% of the genome size (--gsize). Homo sapience - 2700 Mbp Mus musculus - 1870 Mbp Caenorhabditis elegans - 90 Mbp Drosophila melanogaster - 120 Mbp It's the mappable genome size or effective genome size which is defined as the genome size which can be sequenced. Because of the repetitive features on the chromosomes, the actual mappable genome size will be smaller than the original size, about 90% or 70% of the genome size (--gsize). P-value P-value P-value cutoff. Default is 0.00001, for looser results, try 0.001 instead (--pvalue). P-value cutoff. Default is 0.00001, for looser results, try 0.001 instead (--pvalue). Q-value Q-value Minimum FDR (q-value) cutoff for peak detection. Minimum FDR (q-value) cutoff for peak detection. Use model Use model Whether or not to use MACS paired peaks model (--nomodel). Whether or not to use MACS paired peaks model (--nomodel). Model fold Model fold Select the regions within MFOLD range of high-confidence enrichment ratio against. Model fold is available when Use model is true, which is the foldchange to chose paired peaks to build paired peaks model. Users need to set a lower(smaller) and upper(larger) number for fold change so that MACS will only use the peaks within these foldchange range to build model (--mfold). Select the regions within MFOLD range of high-confidence enrichment ratio against. Model fold is available when Use model is true, which is the foldchange to chose paired peaks to build paired peaks model. Users need to set a lower(smaller) and upper(larger) number for fold change so that MACS will only use the peaks within these foldchange range to build model (--mfold). Shift size Shift size An arbitrary shift value used as a half of the fragment size when model is not built. Shift size is available when Use model is false, which will represent the HALF of the fragment size of your sample. If your sonication and size selection size is 300 bps, after you trim out nearly 100 bps adapters, the fragment size is about 200 bps, so you can specify 100 here (--shiftsize). An arbitrary shift value used as a half of the fragment size when model is not built. Shift size is available when Use model is false, which will represent the HALF of the fragment size of your sample. If your sonication and size selection size is 300 bps, after you trim out nearly 100 bps adapters, the fragment size is about 200 bps, so you can specify 100 here (--shiftsize). Keep duplicates Keep duplicates It controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The default auto option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff; and the all option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location (--keep-dup). It controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The default auto option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff; and the all option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location (--keep-dup). Band width Band width The band width which is used to scan the genome for model building. You can set this parameter as the sonication fragment size expected from wet experiment. Used only while building the shifting model (--bw). The band width which is used to scan the genome for model building. You can set this parameter as the sonication fragment size expected from wet experiment. Used only while building the shifting model (--bw). Extended fragment pileup Extended fragment pileup Whether or not to generate extended fragment pileup, local lambda and score tracks at every bp. Whether or not to generate extended fragment pileup, local lambda and score tracks at every bp. Tag size (optional) Tag size (optional) Length of reads. Determined from first 10 reads if not specified (input 0) (--tsize). Length of reads. Determined from first 10 reads if not specified (input 0) (--tsize). Use lambda Use lambda Whether to use local lambda model which can use the local bias at peak regions to throw out false positives (--nolambda). Whether to use local lambda model which can use the local bias at peak regions to throw out false positives (--nolambda). Small nearby region Small nearby region The small nearby region in basepairs to calculate dynamic lambda. This is used to capture the bias near the peak summit region. Invalid if there is no control data (--slocal). The small nearby region in basepairs to calculate dynamic lambda. This is used to capture the bias near the peak summit region. Invalid if there is no control data (--slocal). Large nearby region Large nearby region The large nearby region in basepairs to calculate dynamic lambda. This is used to capture the surround bias (--llocal). The large nearby region in basepairs to calculate dynamic lambda. This is used to capture the surround bias (--llocal). Auto bimodal Auto bimodal Whether turn on the auto pair model process.If set, when MACS failed to build paired model, it will use the nomodelsettings, the “Shift size” parameter to shift and extend each tags (--on-auto). Whether turn on the auto pair model process.If set, when MACS failed to build paired model, it will use the nomodelsettings, the âShift sizeâ parameter to shift and extend each tags (--on-auto). Whether turn on the auto pair model process.If set, when MACS failed to build paired model, it will use the nomodelsettings, the Shift size parameter to shift and extend each tags (--on-auto). If set, MACS will try to call broad peaks by linking nearby highly enriched regions.The linking region is controlled by another cutoff through âBroad cutoffâ.The maximum linking region length is 4 times of d from MACS. If set, MACS will try to call broad peaks by linking nearby highly enriched regions.The linking region is controlled by another cutoff through Broad cutoff. The maximum linking region length is 4 times of d from MACS. Cutoff for broad region. This option is not available unless âBroadâ is set.If âP-valueâ is set, this is a pvalue cutoff, otherwise, it's a qvalue cutoff. Cutoff for broad region. This option is not available unless Broad is set.If P-value is set, this is a pvalue cutoff, otherwise, it's a qvalue cutoff. Scale to large Scale to large When set, scale the small sample up to the bigger sample.By default, the bigger dataset will be scaled down towards the smaller dataset,which will lead to smaller p/qvalues and more specific results.Keep in mind that scaling down will bring down background noise more (--to-large). When set, scale the small sample up to the bigger sample.By default, the bigger dataset will be scaled down towards the smaller dataset,which will lead to smaller p/qvalues and more specific results.Keep in mind that scaling down will bring down background noise more (--to-large). Shift control Shift control When set, control tags will be shifted just as ChIP tags according to their strand before the extension of d, slocal and llocal. By default, control tags are extended centeredat their current positions regardless of strand. You may consider to turn this option on whilecomparing two ChIP datasets of different condition but the same factor. When set, control tags will be shifted just as ChIP tags according to their strand before the extension of d, slocal and llocal. By default, control tags are extended centeredat their current positions regardless of strand. You may consider to turn this option on whilecomparing two ChIP datasets of different condition but the same factor. Half-extend Half-extend When set, MACS extends 1/2 d size for each fragment centered at its middle point. When set, MACS extends 1/2 d size for each fragment centered at its middle point. Broad Broad If set, MACS will try to call broad peaks by linking nearby highly enriched regions.The linking region is controlled by another cutoff through “Broad cutoff”.The maximum linking region length is 4 times of d from MACS. Broad cutoff Broad cutoff Cutoff for broad region. This option is not available unless “Broad” is set.If “P-value” is set, this is a pvalue cutoff, otherwise, it's a qvalue cutoff. Find Peaks with MACS Find Peaks with MACS Performs peak calling for ChIP-Seq data. Performs peak calling for ChIP-Seq data. U2::LocalWorkflow::MAFFTPrompter from %1 from %1 Aligns each MSA supplied %1 with "MAFFT". Aligns each MSA supplied %1 with "MAFFT". U2::LocalWorkflow::MAFFTWorker Input MSA Input MSA Multiple sequence alignment to be processed. Multiple sequence alignment to be processed. Multiple sequence alignment Multiple sequence alignment Result of alignment. Result of alignment. Gap Open Penalty Gap Open Penalty Gap Open Penalty. Gap Open Penalty. Offset Offset Works like gap extension penalty. Works like gap extension penalty. Maximum number of iterative refinement. Maximum number of iterative refinement. External tool path. External tool path. Folder for temporary files. Folder for temporary files. An empty MSA '%1' has been supplied to MAFFT. An empty MSA '%1' has been supplied to MAFFT. Max Iteration Max Iteration Tool Path Tool Path Temporary folder Temporary folder Align with MAFFT Align with MAFFT Aligned %1 with MAFFT Aligned %1 with MAFFT MAFFT is a multiple sequence alignment program for unix-like operating systems. <dfn>It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~10,000 sequences), etc. </dfn> MAFFT is a multiple sequence alignment program for unix-like operating systems. <dfn>It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~10,000 sequences), etc. </dfn> U2::LocalWorkflow::Peak2GenePrompter unset unset Uses annotations from %1 as peak regions Uses annotations from %1 as peak regions to annotate with genes nearby from %1. to annotate with genes nearby from %1. U2::LocalWorkflow::Peak2GeneWorker Treatment features Treatment features Result peaks of MACS. Result peaks of MACS. Peak2gene data Peak2gene data MACS peaks to get the refgenes near the peak summit/center. MACS peaks to get the refgenes near the peak summit/center. Gene regions Gene regions Annotation for each gene, containing all the peaks nearby. Annotation for each gene, containing all the peaks nearby. Peak regions Peak regions Annotation for each peak, containing all the genes nearby. Annotation for each peak, containing all the genes nearby. Gene regions URL URL to file with annotation for each gene, containing all the peaks nearby. Peak regions URL URL to file with annotation for each peak, containing all the genes nearby. Peak2gene output data Peak2gene output data Genes containing all the peaks nearby and peaks containing all the genes nearby. Genes containing all the peaks nearby and peaks containing all the genes nearby. Output type Output type Select which type of genes need to output. up for genes upstream to peak summit, down for genes downstream to peak summit, all for both up and down (--op). Select which type of genes need to output. up for genes upstream to peak summit, down for genes downstream to peak summit, all for both up and down (--op). Official gene symbols Official gene symbols Output official gene symbol instead of refseq name (--symbol). Output official gene symbol instead of refseq name (--symbol). Distance Distance Set a number which unit is base. It will get the refGenes in n bases from peak center (--distance). Set a number which unit is base. It will get the refGenes in n bases from peak center (--distance). Genome file Genome file Select a genome file (sqlite3 file) to search refGenes (--genome). Select a genome file (sqlite3 file) to search refGenes (--genome). Annotate Peaks with peak2gene Annotate Peaks with peak2gene Gets refGenes near the ChIP regions identified by a peak-caller. Gets refGenes near the ChIP regions identified by a peak-caller. U2::LocalWorkflow::SeqPosComboBoxWithChecksDelegate Hint: Hint: Use 'cistrome.xml' to descrease the computation time. It is a comprehensive collection of motifs from the other databases with similar motifs deleted. Use 'cistrome.xml' to descrease the computation time. It is a comprehensive collection of motifs from the other databases with similar motifs deleted. U2::LocalWorkflow::SeqPosPrompter unset unset Uses regions from %1 to find motifs enriched in them. Uses regions from %1 to find motifs enriched in them. Genome assembly: %1. Genome assembly: %1. Finds de novo motifs. Finds de novo motifs. Uses %1 known motifs. Uses %1 known motifs. Outputs all result files to %1 folder Outputs all result files to %1 folder U2::LocalWorkflow::SeqPosWorker Input regions Input regions Peak summits. Peak summits. SeqPos data SeqPos data Finds motifs enriched in a set of regions. Finds motifs enriched in a set of regions. Output folder Output folder The folder to store seqpos results. The folder to store seqpos results. Genome assembly version Genome assembly version UCSC database version (GENOME). UCSC database version (GENOME). De novo motifs De novo motifs Run de novo motif search (-d). Run de novo motif search (-d). Motif database Motif database Known motif collections (-m). Warning: computation time increases with selecting additional databases. It is recommended to use cistrome.xml. It is a comprehensive collection of motifs from the other databases with similar motifs deleted. Known motif collections (-m). Warning: computation time increases with selecting additional databases. It is recommended to use cistrome.xml. It is a comprehensive collection of motifs from the other databases with similar motifs deleted. Output file name Output file name Name of the output file which stores new motifs found during a de novo search (-n). Name of the output file which stores new motifs found during a de novo search (-n). Region width Region width Width of the region to be scanned for motifs; depends on a resolution of assay (-w). Width of the region to be scanned for motifs; depends on a resolution of assay (-w). Pvalue cutoff Pvalue cutoff Pvalue cutoff for the motif significance (-p). Pvalue cutoff for the motif significance (-p). Collect Motifs with SeqPos Collect Motifs with SeqPos U2::LocalWorkflow::ShortReadsAlignerPrompter unset unset Aligns upstream oriented reads from %1 and downstream oriented reads from %2 Aligns upstream oriented reads from %1 and downstream oriented reads from %2 Aligns reads from %1 Aligns reads from %1 to reference genome %1. to reference genome %1. U2::LocalWorkflow::SlopbedPrompter unset unset from %1 from %1 Increases the size of each feature in files from %1 with bedtool slop. Increases the size of each feature in files from %1 with bedtool slop. U2::LocalWorkflow::SlopbedWorker slopBed slopBed Increases the size of each feature in files using bedtools slop. Increases the size of each feature in files using bedtools slop. Input File Input File Set of files to bedtools slop Set of files to bedtools slop Output File Output File Output file Output file Output folder Output folder Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Custom folder Custom folder Select the custom output folder. Select the custom output folder. Output file name Output file name A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. Genome Genome In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. The format of the file is: <chromName><TAB><chromSize> (-g). In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. The format of the file is: <chromName><TAB><chromSize> (-g). Each direction increase Each direction increase Increase the BED/GFF/VCF entry by the same number base pairs in each direction. If this parameter is used -l and -l are ignored. Enter 0 to disable. (-b) Increase the BED/GFF/VCF entry by the same number base pairs in each direction. If this parameter is used -l and -l are ignored. Enter 0 to disable. (-b) Substract from start Substract from start The number of base pairs to subtract from the start coordinate. Enter 0 to disable. (-l) The number of base pairs to subtract from the start coordinate. Enter 0 to disable. (-l) Add to end Add to end The number of base pairs to add to the end coordinate. Enter 0 to disable. (-r) The number of base pairs to add to the end coordinate. Enter 0 to disable. (-r) Strand-based Strand-based Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s) Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s) As fraction As fraction Define -l and -r as a fraction of the featureâs length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp âupstreamâ. (-pct) Define -l and -r as a fraction of the featureâs length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp â upstreamâ. (-pct) Print header Print header Print the header from the input file prior to results. (-header) Print the header from the input file prior to results. (-header) Filter start>end fields Filter start>end fields Remove lines with start postion greater than end position Remove lines with start postion greater than end position Custom Custom Input file Input file Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct) Workflow Workflow U2::LocalWorkflow::SnpEffDatabaseDialog Select Cancel Cancel U2::LocalWorkflow::SnpEffDatabasePropertyWidget Select genome The list of %1 genomes is not available. Path for %1 tool is not selected. Do you want to select it now? Do you want to select it now? U2::LocalWorkflow::SnpEffPrompter unset unset from %1 from %1 Annotates and filters variations %1 with SnpEff. Annotates and filters variations %1 with SnpEff. U2::LocalWorkflow::SnpEffWorker SnpEff Annotation and Filtration SnpEff Annotation and Filtration Annotates and filters variations with SnpEff. Annotates and filters variations with SnpEff. Variations Variations Set of variations Set of variations Annotated variations Annotated variations Output folder Output folder Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Select an output folder. Custom - specify the output folder in the 'Custom folder' parameter. Workflow - internal workflow folder. Input file - the folder of the input file. Custom folder Custom folder Select the custom output folder. Select the custom output folder. Input format Input format Select the input format of variations. Select the input format of variations. Output format Output format Select the format of annotated output files. Select the format of annotated output files. Genome Genome Select the target genome. Genome data will be downloaded if it is not found. Select the target genome. Genome data will be downloaded if it is not found. Upstream/downstream length Upstream/downstream length Upstream and downstream interval size. Eliminate any upstream and downstream effect by using 0 length Upstream and downstream interval size. Eliminate any upstream and downstream effect by using 0 length Canonical transcripts Canonical transcripts Use only canonical transcripts Use only canonical transcripts HGVS nomenclature HGVS nomenclature Annotate using HGVS nomenclature Annotate using HGVS nomenclature Annotate Loss of function variations Annotate Loss of function variations Annotate Loss of function variations (LOF) and Nonsense mediated decay (NMD) Annotate Loss of function variations (LOF) and Nonsense mediated decay (NMD) Annotate TFBSs motifs Annotate TFBSs motifs Annotate transcription factor binding site motifs (only available for latest GRCh37) Annotate transcription factor binding site motifs (only available for latest GRCh37) Input file Input file Workflow Workflow Custom Custom U2::LocalWorkflow::SpadesPrompter unset unset Assemble reads from %1. Assemble reads from %1. U2::LocalWorkflow::SpadesWorker SPAdes cannot recognize read pairs from the same file. Please, perform demultiplexing first. SPAdes cannot recognize read pairs from the same file. Please, perform demultiplexing first. URL of a file with reads URL of a file with reads Input reads to be assembled. Input reads to be assembled. URL of a file with right pair reads URL of a file with right pair reads Input right pair reads to be assembled. Input right pair reads to be assembled. SPAdes data SPAdes data Input reads to be assembled with Spades. Input reads to be assembled with Spades. Scaffolds URL Scaffolds URL Output scaffolds URL. Output scaffolds URL. SPAdes output data SPAdes output data Output assembly files. Output assembly files. Output folder Output folder Folder to save Spades output files. Folder to save Spades output files. Number of threads Number of threads Number of threads (-t). Number of threads (-t). Memory limit (GB) Memory limit (GB) Memory limit (-m). Memory limit (-m). Dataset type Dataset type Input dataset type. Input dataset type. Running mode Running mode Running mode. Running mode. K-mers K-mers k-mer sizes (-k). k-mer sizes (-k). Assemble genomes with SPAdes Assemble genomes with SPAdes Performes assembly of input short reads. Performes assembly of input short reads. U2::LocalWorkflow::TCoffeePrompter from %1 from %1 For each MSA%1, build the alignment using "T-Coffee" and send it to output. For each MSA%1, build the alignment using "T-Coffee" and send it to output. U2::LocalWorkflow::TCoffeeWorker Input MSA Input MSA Multiple sequence alignment to be processed. Multiple sequence alignment to be processed. Multiple sequence alignment Multiple sequence alignment Result of alignment. Result of alignment. Gap Open Penalty Gap Open Penalty Gap Open Penalty. Must be negative, best matches get a score of 1000. Gap Open Penalty. Must be negative, best matches get a score of 1000. Gap Extension Penalty Gap Extension Penalty Gap Extension Penalty. Positive values give rewards to gaps and prevent the alignment of unrelated segments. Gap Extension Penalty. Positive values give rewards to gaps and prevent the alignment of unrelated segments. Max Iteration Max Iteration Number of iteration on the progressive alignment. 0 - no iteration, -1 - Nseq iterations. Number of iteration on the progressive alignment. 0 - no iteration, -1 - Nseq iterations. Tool Path Tool Path External tool path. External tool path. Folder for temporary file.s Folder for temporary files An empty MSA '%1' has been supplied to T-Coffee. An empty MSA '%1' has been supplied to T-Coffee. Temporary folder Temporary folder folder for temporary file.s Align with T-Coffee T-Coffee is a multiple sequence alignment package. T-Coffee is a multiple sequence alignment package. Aligned %1 with T-Coffee Aligned %1 with T-Coffee U2::LocalWorkflow::TopHatWorker Input reads Input reads Input RNA-Seq reads Input RNA-Seq reads TopHat output TopHat output Accepted hits, junctions, insertions and deletions Accepted hits, junctions, insertions and deletions TopHat input reads. Set this slot empty if you want to align reads directly from a file and specify the "Input reads url" slot. When running TopHat with paired-end reads, this should be the *_1 ("left") set of reads. TopHat input reads. Set this slot empty if you want to align reads directly from a file and specify the "Input reads url" slot. When running TopHat with paired-end reads, this should be the *_1 ("left") set of reads. Input reads url Input reads url TopHat input reads url. When running TopHat with paired-end reads, this should be the *_1 ("left") set of reads. TopHat input reads url. When running TopHat with paired-end reads, this should be the *_1 ("left") set of reads. Input paired reads Input paired reads Set this slot empty if you want to align reads directly from a file and specify the "Input reads url" slot. Only used when running TopHat with paired end reads, and contains the *_2 ("right") set of reads. Reads MUST appear in the same order as the *_1 reads. Set this slot empty if you want to align reads directly from a file and specify the "Input reads url" slot. Only used when running TopHat with paired end reads, and contains the *_2 ("right") set of reads. Reads MUST appear in the same order as the *_1 reads. Input paired reads url Input paired reads url Only used when running TopHat with paired end reads, and contains the *_2 ("right") set of reads. Only used when running TopHat with paired end reads, and contains the *_2 ("right") set of reads. Dataset name Dataset name Use it only when sequences slot(or slots) is specified. Group input reads into chunks for several Tophat runs. Set it empty if you want to run Tophat once for all input reads Use it only when sequences slot(or slots) is specified. Group input reads into chunks for several Tophat runs. Set it empty if you want to run Tophat once for all input reads Accepted hits Accepted hits Accepted hits found by TopHat Accepted hits found by TopHat Sample name Sample name Sample name for running Cuffdiff Sample name for running Cuffdiff Accepted hits url Accepted hits url The url to the assembly file with the accepted hits The url to the assembly file with the accepted hits Find Splice Junctions with TopHat Find Splice Junctions with TopHat TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Output folder Output folder The base name of output folder. It could be modified with a suffix. The base name of output folder. It could be modified with a suffix. Samples map Samples map The map which divide all input datasets into samples. Every sample has the unique name. The map which divide all input datasets into samples. Every sample has the unique name. Bowtie index folder Bowtie index folder The folder with the Bowtie index for the reference sequence. The folder with the Bowtie index for the reference sequence. Bowtie index basename Bowtie index basename The basename of the Bowtie index for the reference sequence. The basename of the Bowtie index for the reference sequence. Mate inner distance Mate inner distance The expected (mean) inner distance between mate pairs. The expected (mean) inner distance between mate pairs. Mate standard deviation Mate standard deviation The standard deviation for the distribution on inner distances between mate pairs. The standard deviation for the distribution on inner distances between mate pairs. Library type Library type Specifies RNA-Seq protocol. Specifies RNA-Seq protocol. No novel junctions No novel junctions Only look for reads across junctions indicated in the supplied GFF or junctions file. This parameter is ignored if Raw junctions or Known transcript file is not set. Only look for reads across junctions indicated in the supplied GFF or junctions file. This parameter is ignored if Raw junctions or Known transcript file is not set. Raw junctions Raw junctions The list of raw junctions. The list of raw junctions. Known transcript file Known transcript file A set of gene model annotations and/or known transcripts. A set of gene model annotations and/or known transcripts. Max multihits Max multihits Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many alignments. Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many alignments. Segment length Segment length Each read is cut up into segments, each at least this long. These segments are mapped independently. Each read is cut up into segments, each at least this long. These segments are mapped independently. Fusion search Fusion search Turn on fusion mapping. Turn on fusion mapping. Transcriptome only Transcriptome only Only align the reads to the transcriptome and report only those mappings as genomic mappings. Only align the reads to the transcriptome and report only those mappings as genomic mappings. Transcriptome max hits Transcriptome max hits Maximum number of mappings allowed for a read, when aligned to the transcriptome (any reads found with more than this number of mappings will be discarded). Maximum number of mappings allowed for a read, when aligned to the transcriptome (any reads found with more than this number of mappings will be discarded). Prefilter multihits Prefilter multihits When mapping reads on the transcriptome, some repetitive or low complexity reads that would be discarded in the context of the genome may appear to align to the transcript sequences and thus may end up reported as mapped to those genes only. This option directs TopHat to first align the reads to the whole genome in order to determine and exclude such multi-mapped reads (according to the value of the Max multihits option). When mapping reads on the transcriptome, some repetitive or low complexity reads that would be discarded in the context of the genome may appear to align to the transcript sequences and thus may end up reported as mapped to those genes only. This option directs TopHat to first align the reads to the whole genome in order to determine and exclude such multi-mapped reads (according to the value of the Max multihits option). Min anchor length Min anchor length The anchor length. TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one read with this many bases on each side. The anchor length. TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one read with this many bases on each side. Splice mismatches Splice mismatches The maximum number of mismatches that may appear in the anchor region of a spliced alignment. The maximum number of mismatches that may appear in the anchor region of a spliced alignment. Read mismatches Read mismatches Final read alignments having more than these many mismatches are discarded. Final read alignments having more than these many mismatches are discarded. Segment mismatches Segment mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. Solexa 1.3 quals Solexa 1.3 quals As of the Illumina GA pipeline version 1.3, quality scores are encoded in Phred-scaled base-64. Use this option for FASTQ files from pipeline 1.3 or later. As of the Illumina GA pipeline version 1.3, quality scores are encoded in Phred-scaled base-64. Use this option for FASTQ files from pipeline 1.3 or later. Bowtie version Bowtie version Specifies which Bowtie version should be used. Specifies which Bowtie version should be used. Bowtie -n mode Bowtie -n mode TopHat uses -v in Bowtie for initial read mapping (the default), but with this option, -n is used instead. Read segments are always mapped using -v option. TopHat uses -v in Bowtie for initial read mapping (the default), but with this option, -n is used instead. Read segments are always mapped using -v option. Bowtie tool path Bowtie tool path The path to the Bowtie external tool. The path to the Bowtie external tool. SAMtools tool path SAMtools tool path The path to the SAMtools tool. Note that the tool is available in the UGENE External Tool Package. The path to the SAMtools tool. Note that the tool is available in the UGENE External Tool Package. TopHat tool path TopHat tool path The path to the TopHat external tool in UGENE. The path to the TopHat external tool in UGENE. Temporary folder Temporary folder The folder for temporary files. The folder for temporary files. Use -n mode Use -v mode Aligns RNA-seq reads to a reference and finds splice junctions. Aligns RNA-seq reads to a reference and finds splice junctions. Incorrect value of the library type parameter for Cufflinks! Incorrect value of the library type parameter for Cufflinks! Unrecognized value of the Bowtie mode option! Unrecognized value of the Bowtie mode option! U2::LocalWorkflow::VcfConsensusPrompter Apply VCF variants from %1 to fasta file %2 and save consensus sequence to %3. Apply VCF variants from %1 to fasta file %2 and save consensus sequence to %3. U2::LocalWorkflow::VcfConsensusWorker Input fasta slot is empty Input fasta slot is empty Input vcf slot is empty Input vcf slot is empty Input FASTA and VCF Input FASTA and VCF FASTA url FASTA url VCF url VCF url Fasta consensus url Fasta consensus url Output FASTA consensus Output FASTA consensus The path to the output file with the result consensus. The path to the output file with the result consensus. Create VCF Consensus Create VCF Consensus Apply VCF variants to a fasta file to create consensus sequence. Apply VCF variants to a fasta file to create consensus sequence. U2::MACSSupport MACS - Model-based Analysis of ChIP-Seq data, which analyzes datagenerated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shiftsize of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites.MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome,allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available. MACS - Model-based Analysis of ChIP-Seq data, which analyzes datagenerated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shiftsize of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites.MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome,allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available. U2::MACSTask MACS peak calling MACS peak calling U2::MAFFTLogParser MAFFT has switched to the memsave mode. UGENE is unable to track its progress. MAFFT has switched to the memsave mode. UGENE is unable to track its progress. U2::MAFFTSupport MAFFT is a multiple sequence alignment program for unix-like operating systems. MAFFT is a multiple sequence alignment program for unix-like operating systems. Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::MAFFTSupportContext Align with MAFFT... Align with MAFFT... Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::MAFFTSupportRunDialog Align Align Cancel Cancel U2::MAFFTSupportTask MAFFT alignment started MAFFT alignment started Saving data to temporary file '%1' Saving data to temporary file '%1' Subdir for temporary files exists. Can not remove this folder. Subdir for temporary files exists. Can not remove this folder. Can not create folder for temporary files. Can not create folder for temporary files. Can not open output file: Can not open output file: May be %1 tool path '%2' not valid? May be %1 tool path '%2' not valid? Output file '%1' not found Output file '%1' not found Output file '%3' not found. May be %1 tool path '%2' not valid? Output file '%3' not found. May be %1 tool path '%2' not valid? Loading output file '%1' Loading output file '%1' Failed to apply the result of aligning with MAFFT: alignment object is not available! Failed to apply the result of aligning with MAFFT: alignment object is not available! MAFFT alignment successfully finished MAFFT alignment successfully finished Can not remove folder for temporary files. Can not remove folder for temporary files. U2::MAFFTWithExtFileSpecifySupportRunDialog Align Align Cancel Cancel Open an alignment file Open an alignment file Save an multiple alignment file Save an multiple alignment file Kalign with Align Align with Kalign Input file is not set! Input file is not set! Output file is not set! Output file is not set! U2::MAFFTWithExtFileSpecifySupportTask Unrecognized input alignment file format Unrecognized input alignment file format U2::MafftAddToAlignmentTask Align sequences to alignment task Align sequences to alignment task Align sequences to an existing alignment by MAFFT started Align sequences to an existing alignment by MAFFT started Output file '%1' not found Output file '%1' not found Output file '%3' not found. May be %1 tool path '%2' not valid? Output file '%3' not found. May be %1 tool path '%2' not valid? Loading output file '%1' Loading output file '%1' Row for updating doesn't found MAFFT alignment successfully finished MAFFT alignment successfully finished U2::MrBayesGetCalculatedTreeTask Generating output trees from MrBayes Generating output trees from MrBayes Output file is not found Output file is not found No trees are found No trees are found U2::MrBayesPrepareDataForCalculation Generating input file for MrBayes Generating input file for MrBayes U2::MrBayesSupport MrBayes is a program for the Bayesian estimation of phylogeny.Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. MrBayes is a program for the Bayesian estimation of phylogeny.Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. U2::MrBayesSupportTask MrBayes tree calculation MrBayes tree calculation U2::MrBayesWidget Substitution model Substitution model Rate Matrix (fixed) Rate Matrix (fixed) Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::PathLineEdit Select a file Select a file U2::Peak2GeneFormatLoader Incorrect start position at line %1: '%2' Incorrect end position at line %1: '%2' Incorrect peak score at line %1: '%2' Incorrect NA value at line %1: '%2' U2::Peak2GeneSupport peak2gene - Gets refGenes near the ChIP regions identified by a peak-caller peak2gene - Gets refGenes near the ChIP regions identified by a peak-caller U2::PerlSupport Perl scripts interpreter Perl scripts interpreter U2::PhmmerSearchDialog Search Search Cancel Cancel Select query sequence file Query sequence file path is empty Error Error Cannot create an annotation object. Please check settings Cannot create an annotation object. Please check settings Error: bad arguments! U2::PhmmerSearchTask Search with phmmer Query sequence: Task was not finished Result annotation table: Result annotation group: Result annotation name: Results count: Cannot create a folder for temporary files. U2::PhyMLGetCalculatedTreeTask Generating output trees from PhyML Generating output trees from PhyML Output file is not found Output file is not found No trees are found No trees are found No result tree in PhyML output No result tree in PhyML output U2::PhyMLLogParser PhyML finished with error PhyML finished with error UGENE internal error UGENE internal error U2::PhyMLPrepareDataForCalculation Generating input file for PhyML Generating input file for PhyML Internal UGENE error Internal UGENE error Can not open tmp file Can not open tmp file U2::PhyMLSupport PhyML is a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood PhyML is a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood U2::PhyMLSupportTask PhyML tree calculation PhyML tree calculation UGENE internal error UGENE internal error U2::PhyMlWidget Open an alignment file Open an alignment file File with the starting tree is not set. File with the starting tree doesn't exist. Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::PrepareInputFastaFilesTask Prepare input FASTA files File '%1' was skipped. Cannot detect the file format. U2::PrepareInputForCAP3Task Failed to initialize sequence writer. Failed to initialize sequence writer. Failed to write sequence %1 Failed to write sequence %1 U2::PrepareInputForSpideyTask Failed to write DNA sequence %1 Failed to write DNA sequence %1 U2::PrepareReferenceSequenceTask Prepare reference sequence No reference sequence in the file: More than one sequence in the reference file: Unable to cast gobject to sequence object The input reference sequence '%1' contains characters that don't belong to DNA alphabet. U2::PythonModuleDjangoSupport : Python module for the %1 tool : Python module for the %1 tool U2::PythonModuleNumpySupport : Python module for the %1 tool : Python module for the %1 tool U2::PythonModuleSupport Python module is not installed. Install module or set path to another Python scripts interpreter with installed module in the External Tools settings Python module is not installed. Install module or set path to another Python scripts interpreter with installed module in the External Tools settings U2::PythonSupport Python scripts interpreter Python scripts interpreter U2::RModuleCelegansdbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleDrosophila2dbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleGodbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleGostatsSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleHgu133adbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleHgu133bdbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleHgu133plus2dbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleHgu95av2dbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleMouse430a2dbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleOrgceegdbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleOrgdmegdbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleOrghsegdbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleOrgmmegdbSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleSeqlogoSupport : Rscript module for the %1 tool : Rscript module for the %1 tool U2::RModuleSupport R module is not installed. Install module or set path to another R scripts interpreter with installed module in the External Tools settings R module is not installed. Install module or set path to another R scripts interpreter with installed module in the External Tools settings U2::RSupport Rscript interpreter Rscript interpreter U2::RemoveGapsFromSequenceTask Remove gaps from the sequence Find gaps in the sequence U2::RunCap3AndOpenResultTask CAP3 run and open result task CAP3 run and open result task Invalid CAP3 task Invalid CAP3 task Project loader is NULL Project loader is NULL U2::SaveAlignmentTask Export alignment to '%1' Export alignment to '%1' An alignment is empty An alignment is empty U2::SaveMSA2SequencesTask Export alignment to sequence: %1 Export alignment to sequence: %1 U2::SaveSequenceTask Save sequence '%' format is not registered U2::SeqPosSupport SeqPos - Finds motifs enriched in a set of regions. SeqPos - Finds motifs enriched in a set of regions. U2::SnpEffDatabaseListModel Genome Genome Organism U2::SnpEffDatabaseListTask SnpEff Database List task U2::SnpEffParser A problem occurred during allocating memory for running SnpEff. Check the "Tasks memory limit" parameter in the UGENE Application Settings.It is recommended to set this value to the available RAM on the computer. There is not enough memory to complete the SnpEff execution.It is recommended to run SnpEff on a computer with RAM 4Gb or more. Failed to download SnpEff database. Check your internet connection. Genome database '%1' is not found. U2::SnpEffSupport SnpEff: Genetic variant annotation and effect prediction toolbox. SnpEff: Genetic variant annotation and effect prediction toolbox. Failed to get SnpEff database list U2::SnpEffTask SNPEff dataDir is not initialized. SNPEff dataDir is not initialized. U2::SpadesSupport SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. Official site: http://bioinf.spbau.ru/spades SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies. Official site: http://bioinf.spbau.ru/spades U2::SpadesTask Folder does not exist: Folder does not exist: U2::SpideyAlignmentTask Output file not found Output file not found Output file not found. May be %1 tool path '%2' not valid? Output file not found. May be %1 tool path '%2' not valid? Failed to open result file %1 Failed to open result file %1 U2::SpideySupport Spidey is mRNA-to-DNA alignment program. Binaries can be downloaded from http://www.ncbi.nlm.nih.gov/spidey/spideyexec.html Spidey is mRNA-to-DNA alignment program. Binaries can be downloaded from http://www.ncbi.nlm.nih.gov/spidey/spideyexec.html Wheelan SJ, Church DM, Ostell JM. Wheelan SJ, Church DM, Ostell JM. Spidey: a tool for mRNA-to-genomic alignments Spidey: a tool for mRNA-to-genomic alignments Genome Res. 2001 Nov;11(11):1952-7. Genome Res. 2001 Nov;11(11):1952-7. U2::SpideySupportContext Align sequence to mRNA Align sequence to mRNA Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::SpideySupportTask Failed to align mRNA to genomic sequence: no alignment is found. Failed to align mRNA to genomic sequence: no alignment is found. U2::TBlastXPlusSupportTask Unexpected settings combination Unexpected settings combination U2::TCoffeeSupport T-Coffee is a multiple sequence alignment package. T-Coffee is a multiple sequence alignment package. Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::TCoffeeSupportContext Align with T-Coffee... Align with T-Coffee... Path for %1 tool not selected. Path for %1 tool not selected. Do you want to select it now? Do you want to select it now? U2::TCoffeeSupportRunDialog Align Align Cancel Cancel U2::TCoffeeSupportTask Unsupported alphabet: %1 Unsupported alphabet: %1 T-Coffee alignment started T-Coffee alignment started Saving data to temporary file '%1' Saving data to temporary file '%1' Subdir for temporary files exists. Can not remove this folder. Subdir for temporary files exists. Can not remove this folder. Can not create folder for temporary files. Can not create folder for temporary files. Output file %1 not found Output file %1 not found Output file %3 not found. May be %1 tool path '%2' not valid? Output file %3 not found. May be %1 tool path '%2' not valid? Loading output file '%1' Loading output file '%1' Failed to apply the result of TCoffee: alignment object is not available! Failed to apply the result of TCoffee: alignment object is not available! T-Coffee alignment successfully finished T-Coffee alignment successfully finished Can not remove folder for temporary files. Can not remove folder for temporary files. U2::TCoffeeWithExtFileSpecifySupportRunDialog Align Align Cancel Cancel Open an alignment file Open an alignment file Save an multiple alignment file Save an multiple alignment file Kalign with Align Align with Kalign Input file is not set! Input file is not set! Output file is not set! Output file is not set! U2::TCoffeeWithExtFileSpecifySupportTask Unrecognized input alignment file format Unrecognized input alignment file format U2::TabixSupport Tabix is a generic indexer for TAB-delimited genome position files Tabix is a generic indexer for TAB-delimited genome position files U2::TabixSupportTask Generate index with Tabix task Generate index with Tabix task Tabix indexing started Tabix indexing started Input file '%1' is already bgzipped Input file '%1' is already bgzipped Saving data to file '%1' Saving data to file '%1' U2::TabulatedFormatReader IO adapter is not opened U2::TopHatSupportTask Running TopHat task Running TopHat task An unexpected error has occurred during preparing the TopHat task! An unexpected error has occurred during preparing the TopHat task! Preparing TopHatSupportTask internal error: unable to get a sequence object! Preparing TopHatSupportTask internal error: unable to get a sequence object! TopHat was not able to map reads to the reference. There are no accepted hits in the result There are no accepted hits in the result U2::UserAppsSettings Temporary UGENE dir is empty Temporary UGENE dir is empty U2::VcfConsensusSupport Apply VCF variants to a fasta file to create consensus sequence. Apply VCF variants to a fasta file to create consensus sequence. U2::VcfConsensusSupportTask Create Vcf Consensus Create Vcf Consensus VcfConsensus started VcfConsensus started AppSettings is NULL AppSettings is NULL UserAppsSettings is NULL UserAppsSettings is NULL Temporary folder is not set! Temporary folder is not set! Can not create folder for temporary files. Can not create folder for temporary files. Saving temporary data to file '%1' Saving temporary data to file '%1' ExternalToolRegistry is NULL ExternalToolRegistry is NULL There is no VcfConsensus external tool registered There is no VcfConsensus external tool registered There is no Tabix external tool registered There is no Tabix external tool registered Trying to get path of NULL external tool Trying to get path of NULL external tool Path to %1 Path to %1 U2::Workflow::BlastAndSwReadTask Map one read with BLAST & SW task A problem occurred while mapping "%1" to "%2". %1 was skipped. No BLAST results. %1 was skipped. Low similarity: %2. Minimum similarity was set to %3 Read doesn't contain meaningful data The %1 algorithm is not found. Add the %1 plugin. The %1 algorithm is not found. Check that the %1 plugin is up to date. U2::Workflow::BlastReadsSubTask Map reads with BLAST & SW task The task uses a temporary folder to process the data. The folder path is required not to have spaces. Please set up an appropriate path for the "Temporary files" parameter on the "Directories" tab of the UGENE Application Settings. U2::Workflow::ComposeResultSubTask Compose alignment No read satisfy minimum similarity criteria. The related chromatogram not found U2::Workflow::FormatDBSubTask Format DB task wrapper The task uses a temporary folder to process the data. It is required that the folder path doesn't have spaces. Please set up an appropriate path for the "Temporary files" parameter on the "Directories" tab of the UGENE Application Settings. U2::Workflow::IntegralBusPort '%1' slot must be not binded '%1' slot must be not binded One of these slots must be not empty: '%1', '%2' One of these slots must be not empty: '%1', '%2' Only one of these slots must be binded: '%1', '%2' Only one of these slots must be binded: '%1', '%2' The slot must be not empty: '%1' The slot must be not empty: '%1' Error! One of these slots must be not empty: '%1', '%2' Error! One of these slots must be not empty: '%1', '%2' Error! You can not bind one of sequences slots and one of url slots simultaneously Error! You can not bind one of sequences slots and one of url slots simultaneously UserAppsSettings Temporary UGENE dir is empty Temporary UGENE dir is empty