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/
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