Hi Martin, Regarding this part of your question:
> > By the way, can I / should I use any format other than PSL for a > > custom track of translated alignments? I tried MAF, but it didn't > > work. It would be nice if I could click on a track item and see the > > alignment. It would be nice if stop codons and frameshifts were > > highlighted in red or something, is it possible to do that? We don't have another format specifically for translated alignments. Did MAF not work for you because it is a nucleotide-level format, or some other reason? If you do have nucleotide-level alignments, and can output the BAM format (http://genome.ucsc.edu/goldenPath/help/bam.html), nucleotide-level differences are highlighted in the same way as hgBlat untranslated results. It would be a non-trivial enhancement to highlight codon differences in PSL custom tracks -- we would need to add a way for you to upload query sequences associated with your alignments (and for nucleotide-level PSL, CDS start and stop for each query), and we don't yet display translated differences even in in hgBlat results. That would be very cool, but we all have pretty full plates here already. Angie ----- "Galt Barber" <[email protected]> wrote: > From: "Galt Barber" <[email protected]> > To: "Martin Frith" <[email protected]> > Cc: [email protected] > Sent: Tuesday, October 19, 2010 4:43:36 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] custom track: translated psl strand bug > > Hi, Martin! > > This does seem to be a bug in the PSL customTrack loader. > It should mark the strand as "-" instead of "+". > We will look into it. > > Currently we convert PSL custom tracks to bed12. > So it really can't show un-aligned parts. > > The BLAT track (hgBlat) does a much better job > of showing more details about the alignment. > > Thank you for reporting the problem. > > -Galt > > 10/18/2010 7:05 PM, Martin Frith: > > Dear genome folks, > > > > I would like to display a custom track of protein-versus-genome > > alignments. I tried using PSL format, but there seems to be a bug > > with "-" strands. > > > > For example, I blatted this sequence against hg19 with "output > type" > > set to hyperlink: > > LSVADHAPQFAVPSDTATAPQAESVLRPLYMDVQATTPL > > > > The output looks like this: > > SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN > > 63 1 39 39 77.0% 20 +- 34286403 34286519 > 117 > > When I view it in the browser, the arrows go right-to-left, which > is > > correct. > > > > I repeated this blat with "output type" set to psl: > > match mis- rep. N's Q gap Q gap T gap T gap > strand ... > > match match count bases count bases > ... > > 30 9 0 0 0 0 0 0 +- > ... > > I then pasted this PSL line into "add custom tracks". > > When I view it in the browser, the arrows go left-to-right, which > > seems wrong. > > > > > > By the way, can I / should I use any format other than PSL for a > > custom track of translated alignments? I tried MAF, but it didn't > > work. It would be nice if I could click on a track item and see > the > > alignment. It would be nice if stop codons and frameshifts were > > highlighted in red or something, is it possible to do that? > > > > Have a nice day, > > Martin Frith > > http://www.cbrc.jp/~martin/ > > _______________________________________________ > > 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
