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Commit message:
planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty |
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modified:
blat.xml |
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| diff -r 6f06b6d68c0b -r bd3352c46beb blat.xml --- a/blat.xml Wed Feb 01 17:52:37 2017 -0500 +++ b/blat.xml Wed Feb 01 18:03:17 2017 -0500 |
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| @@ -124,31 +124,43 @@ BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. blat (version: v340)- Standalone blat sequence search command line tool. ---------------------------------------------------------- +------------------------------------------------------------------------- + usage: ++++++ - blat database query [-ooc=11.ooc] output.psl + + $ blat database query [-ooc=11.ooc] output.psl + where: database and query are each either a .fa, .nib or .2bit file, - or a list of these files with one file name per line. + or a list of these files with one file name per line. -ooc=11.ooc tells the program to load over-occurring 11-mers from - an external file. This will increase the speed - by a factor of 40 in many cases, but is not required. - output.psl is the name of the output file. + an external file. This will increase the speed + by a factor of 40 in many cases, but is not required. + output.psl is the name of the output file. + documentation: ++++++++++++++ -See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) + +See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) + Source code: ++++++++++++ + http://hgdownload.cse.ucsc.edu/admin/exe/ + pslCDnaFilter (version: v340) ---------------------------- +----------------------------- Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment. + usage: ++++++ - pslCDnaFilter [options] inPsl outPsl + + $ pslCDnaFilter [options] inPsl outPsl + Source code: ++++++++++++ + http://hgdownload.cse.ucsc.edu/admin/exe/ Licence |