Hi Elliott, Sorry, we don't support that for PSL/pslx custom tracks at this point. However, we do show differences for MAF custom tracks (http://hgwdev-angie.cse.ucsc.edu/FAQ/FAQformat.html#format5), and blat can write MAF as output (-out=maf).
BAM custom tracks show base differences, look more like the native-track PSL display, and only the needed parts are uploaded (like bigWig and bigBed), but psl to BAM conversion is more work than it should be (http://generic-model-organism-system-database.450254.n5.nabble.com/Getting-sequences-into-a-BAM-file-td454848.html). We have a to-do item to make a PSL to bam converter, but unfortunately there are many higher-priority items so I can't say when we'll get to that. Hope that helps and please let us know if you have more questions, Angie ----- "Elliott H Margulies" <[email protected]> wrote: > From: "Elliott H Margulies" <[email protected]> > To: [email protected] > Sent: Tuesday, January 25, 2011 9:58:35 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] viewing blat results > > Hello Genome Browser Friends, > > I have a blat/psl question for you: If I run blat on your server, it > displays my alignments with some more enhanced features that I really > like. When you zoom out, it draws lines where there are > differences. When you're zoomed in at basepair level, it shows the base > difference. However, if I upload a psl (or pslx) file from running blat > locally, it doesn't show these features. Is it possible to get the > enhanced view from a locally run blat via custom tracks or other > tweak? > > Thanks, > Elliott > > -- > Elliott H. Margulies, Ph.D. > Investigator, Genome Technology Branch > Head, Genome Informatics Section > National Human Genome Research Institute > National Institutes of Health > 5625 Fishers Lane > Room 5N-01N, MSC9400 > Bethesda, MD 20892 > * > phone: (301) 594-9210 > fax: (301) 480-3520 > http://genome.gov/staff/margulies/ > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
