Hi Angie, Thanks for the quick response.
I converted the bed to bam because I wanted to use some data I pulled down from GEO that is supposed to represent alignments, but was only given as bed files. The tools I've written to deal with NGS data work off of bam files, so I thought the easiest thing to do was to convert it to a bam file and move along -- and my collaborator likes to look at data through the "UCSC Genome Browser lens", which is where I got tripped up. Converting the data to bigBed didn't even cross my mind, really ... I regenerated bam files from the bed files, but put NNN's in the SEQ column for now. Thanks for the help, -steve On Fri, Jul 29, 2011 at 7:20 PM, Angie Hinrichs <[email protected]> wrote: > Hi Steve, > > You're right -- that is legal BAM, but our code expects to see a query > sequence that corresponds to the CIGAR (in this case, it wants 32 bases > corresponding to "32M"). The code assumes that BAM contains sequence > alignments. Thanks for reporting this, I will work on a fix. > > In the meantime, can you tell us why you converted bed to bam? The bigBed > format (http://genome.ucsc.edu/goldenPath/help/bigBed.html) was designed for > large remote BED tracks, and might be a better solution (at least for viewing > in the genome browser :). > > Thanks, > Angie > > ----- Original Message ----- > From: "Steve Lianoglou" <[email protected]> > To: [email protected] > Sent: Friday, July 29, 2011 2:48:45 PM > Subject: Re: [Genome] Mimimal BAM files is tripping up browser > > As a follow up to this -- I think the "*" in either the sequence or > quality columns (columns 10 or 11) of a BAM file is what's causing the > error ... > > -steve > > On Fri, Jul 29, 2011 at 4:59 PM, Steve Lianoglou > <[email protected]> wrote: >> Hi, >> >> [sorry, I sent this email to the genome-mirror list previously, so I'm >> resending here] >> >> I've converted some bed files to bam files using bedtools. >> >> The alignments in the bam file look like so: >> >> * 16 chr1 13517 255 32M * 0 0 >> * * >> * 16 chr1 16275 255 32M * 0 0 >> * * >> * 16 chr1 16458 255 32M * 0 0 >> * * >> * 16 chr1 16461 255 32M * 0 0 >> * * >> >> When I add the bam file as a custom track and try to hop to the >> genome, I get this error: >> >> baseColorDrawSetup: *: mRNA size (0) != psl qSize (32) >> >> I've put this BAM file online to help smoke this problem for testing >> purposes, which you can add as a custom track like so: >> >> track type="bam" name="test-bam" >> bigDataUrl="http://cbio.mskcc.org/leslielab/files/ucsc/test.bam"; >> genome="hg19" visibility="squish" >> >> I'm guessing that the genome browser doesn't like "*" in the QNAME >> (1st) column of the BAM file (or maybe one of the "*"s in another >> column(?)). >> >> It's easy enough for me to change whatever column to a bogus value to >> fix this (some points as to which column that would be are welcome), >> but as far as I can tell this is a valid bam file. Each column that >> has a "*" is allowed to do so according to the spec: >> >> http://samtools.sourceforge.net/SAM1.pdf >> >> While this is easy enough for me to fix on my end, I thought it would >> be worth reporting since it seems like a (somehow minor) bug on your >> side as well (assuming such a bam file is valid, of course). >> >> Thanks, >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> > > > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
