Update: One more utility that you may find useful: pslStats
Thanks! jennifer On 5/12/10 10:55 AM, Jennifer Jackson wrote: > Hello - > > The program pslCoverage is fairly old and is not recommended for use > anymore. > > We are curious about what exactly you are trying to do so that we can > offer appropriate help: > 1) comparing known mRna/cDna sequences to each genome? > 2) comparing the genomes to each other? In preparation for a chain/net > track? > 3) comparing the genomes to a third genome? In preparation for a > conservation track? > > FYI - for general BLAT filtering, we recommend using pslCDnaFilter > and/or pslReps, then calculating the percentID yourself from the > available stats. > > Please let us know more details of your analysis and we can try to offer > more help, if needed, > > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/11/10 2:12 PM, rayann siri wrote: >> >> Dear UCSC support team, >> I use some "UCSC Genome Browser" softwares, and I would need to know a >> little more about "pslCoverage" tool. >> >> I want to determine the coverages of my alignments of two species of >> Arabidopsis, percentages of identity, and calculate an average. The "psl >> output" format I get with Blat does not give these informations. >> >> For the percentage of identity, i used the "-out=blast9" option, but little >> information is available on a "pslCoverage" tool. When i type the command >> without argument i have this : usage: pslCoverage in.sizes in.psl >> minPercentId endTrim out.cov misAsm.out. >> >> What is "endTrim", "misAsm", and minPercentId? >> >> Thank you very much for your help >> >> _________________________________________________________________ >> Découvrez Windows Phone 7 : Une nouvelle ère de téléphones ! >> http://www.microsoft.com/windowsmobile/fr-fr/cmpn1/windowsphone7series/default.mspx >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
