Mercurial > repos > yating-l > ucsc_pslcdnafilter
changeset 1:ad9a21204405 draft default tip
planemo upload commit 46cd27d5fb1b88220fb94b9039a685359b87d539
| author | yating-l |
|---|---|
| date | Thu, 02 Feb 2017 17:06:45 -0500 |
| parents | 34c6f02de27f |
| children | |
| files | README.rst |
| diffstat | 1 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Feb 02 17:06:45 2017 -0500 @@ -0,0 +1,57 @@ +Galaxy wrapper for UCSC pslCDnaFilter tool (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. + +parameters: +----------- +pslCDnaFilter parameters variable definitions by genome assembly category and type of cDNA sequence. + +# common paramters used for all assembly categories + +Same species: + -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes + +Across species: + -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes + +# common paramters used for local near best filtering + +Same species: + -localNearBest=0.001 +Across species: + -localNearBest=0.010 + +# finished assemblies + +Same species: + -minId=0.95 -minCover=0.25 +Across species: + -minId=0.35 -minCover=0.25 + +# well-ordered assemblies + +Same species: + -minId=0.95 -minCover=0.15 +Across species: + -minId=0.35 -minCover=0.15 + +# low-coverage assemblies + +Same species: + -minId=0.94 -minAlnSize=80 +Across species: + -minId=0.33 -minAlnSize=80 + +Reference: +++++++++++ +`Configuration file for GenBank RefSeq alignment process <http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/genbank/etc/genbank.conf;h=03c4f3dcd12b48cf52feaf4d09561bf0a58ee352;hb=9447c3aa53839f2adbb3c2ef14ba8540a1dea077>`_ + + +Source code: +------------- + +http://hgdownload.cse.ucsc.edu/admin/exe/ + +Licence +------- +Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).