Thanks Vanessa. Is it possible to emulate this sort of display with any of the custom track formats available?
I have looked into it somewhat and none of the custom track formats seem to support multiple colours in a single track line. Does webBLAT use pslx formatted data for the tracks it displays in the Genome Browser? Can custom tracks be in pslx format? ~Thanks, Lucas Vanessa Kirkup Swing wrote: > 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" <[email protected]> > To: [email protected] > 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 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
