Hi Max and Lucas, > psl2sam.pl in samtools might be a good starting point (though I guess > it's not the complete answer as it does not parse the fasta file):
This thread offers a couple alternative scripts to include the fasta: http://generic-model-organism-system-database.450254.n5.nabble.com/Getting-sequences-into-a-BAM-file-td454848.html Cheers, Angie ----- "Maximilian Haussler" <[email protected]> wrote: > From: "Maximilian Haussler" <[email protected]> > To: "Mary Goldman" <[email protected]> > Cc: [email protected] > Sent: Friday, July 30, 2010 2:23:53 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Custom Tracks Resembling WebBLAT Alignments > > Hi Lucas, > psl2sam.pl in samtools might be a good starting point (though I guess > it's not the complete answer as it does not parse the fasta file): > http://samtools.svn.sourceforge.net/viewvc/samtools/trunk/samtools/misc/psl2sam.pl?revision=423&view=markup > > You could then convert from sam to bam with samtools. > > cheers > Max > > On Fri, Jul 30, 2010 at 1:55 AM, Mary Goldman <[email protected]> > wrote: > > > > 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 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
