Thanks, this sounds like what I am looking for! ~Lucas
Angie Hinrichs wrote: > 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
