Hi Lucas, In order to see alignment coloring, you need to have the sequence. WebBlat generates a psl plus a fasta file containing the original sequence, which is uses to display the alignment. Unfortunately, we do not support pslx formats as custom tracks. However, if you turn can your psl file and fasta file into a BAM file, then you should be able to see all of the alignment coloring available in webBlat. This page should help you get started: http://genome.ucsc.edu/goldenPath/help/bam.html.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 7/29/10 11:43 AM, Lucas Swanson wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
