Hi, Martin! This has been fixed in customFactory.c and you should see it in the next release which will be v244.
Thanks again for reporting this. -Galt 10/19/2010 4:43 PM, Galt Barber: > > 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
