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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
