Dear Lucas,
Unfortunately, we don't support this in psl customTracks because the plain psl
does not have the necessary information for a detailed alignment, i.e. where
every substitution is.
Please don't hesitate to contact the mailing list if you have further questions.
Vanessa Kirkup Swing
UCSC Genome Bioinformatics Group
----- Original Message -----
From: "Lucas Swanson" <lswan...@bcgsc.ca>
To: gen...@soe.ucsc.edu
Sent: Tuesday, July 27, 2010 5:55:28 PM GMT -08:00 US/Canada Pacific
Subject: [Genome] Custom Tracks Resembling WebBLAT Alignments
Hello,
When webBLAT is used to align a sequence, and then the alignment is
viewed in the Genome Browser,
"alignments of nucleotides use color to highlight differences as follows:
* *red:* Genome and query sequence have different bases at this
position.
* *orange:* The query sequence has an insertion (or genome has a
deletion / alignment gap) at this point.
* *purple:* The query sequence extends beyond the end of the alignment.
* *green:* The query sequence appears to have a polyA tail which is
not aligned to the genome.
Also, when the alignment has gaps for both genome and query sequence,
double horizontal lines are drawn."
However, if command-line BLAT is used to do the alignment, and then the
psl output file added to the Genome Browser as a custom track, all of
this colour and double-line information is lost.
Is there any way to make a custom track that retains this information in
any way?
~Thanks,
Lucas Swanson
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_______________________________________________
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