Hi, Bill. I'm not a UCSC person, but I did take a quick look at your data using:
samtools idxstats http://noble.gs.washington.edu/~ymao/proj/s_6_1.bam It appears from this output that the VAST majority of your reads are not mapped. That probably explains why you do not see any data since, on average, it appears that only a few hundred reads are on any chromosome. Hope that helps. Sean On Thu, Dec 1, 2011 at 3:04 PM, William Noble <[email protected]>wrote: > Hi, > > We are trying to view a BAM file at UCSC, created by Bowtie followed by > Samtools. The file is visible on the web at > > http://noble.gs.washington.edu/~ymao/proj/s_6_1.bam > > However, when we upload this to the mm9 genome in the custom track page, > using this track line > > track type=bam db=mm9 > bigDataUrl=http://noble.gs.washington.edu/~ymao/proj/s_6_1.bam > > we don't actually see any data in the browser. When we instead upload > the file directly, using the "Browse..."/"Upload" option, we get an > error message that says "*Error Can't read file: s_6_1.bam*". > > Since BAM is not text-based, it's not easy to figure out how to debug > this. Can anyone help us figure out what's wrong with our file? > > Bill > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
