Mercurial > repos > yating-l > ucsc_blat
changeset 7:bd3352c46beb draft
planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
| author | yating-l |
|---|---|
| date | Wed, 01 Feb 2017 18:03:17 -0500 |
| parents | 6f06b6d68c0b |
| children | 5e4e16939d3b |
| files | blat.xml |
| diffstat | 1 files changed, 21 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/blat.xml Wed Feb 01 17:52:37 2017 -0500 +++ b/blat.xml Wed Feb 01 18:03:17 2017 -0500 @@ -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