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
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