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
