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
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
