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
