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