Hi Mike, Sorry to hear about the trouble. One possible cause of this symptom is an index file (.bam.bai) that is out of sync with the bigDataUrl bam file. For example, if the bam file is changed, but the .bam.bai file is not regenerated (samtools index my.bam), then the byte offsets in the stale .bam.bai point to incorrect locations in the bam data, and the resulting coordinates from the query are garbage so no items are found in range.
If that doesn't explain your case, please send me a URL off-list so I can try to duplicate the problem and debug. Hope that helps, Angie ----- "Michael Muratet" <[email protected]> wrote: > From: "Michael Muratet" <[email protected]> > To: [email protected] > Sent: Thursday, September 30, 2010 4:04:31 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Paired-end BAM track invisible > > Dear colleagues > > I have created a set of indexed BAM files for single- and paired-end > reads per the FAQ and put them in a directory on a web server where > the genome browser can find them. At one point, it was working > perfectly and I could see all the tracks that I loaded. I tried again > today and now the paired-end tracks are invisible although single- > tracks show up. No error windows pop up, but there's no reads shown at > any scale. > > I changed the name of the file in the bigDataUrl field and did get a > 'file not found' error so it seems like the files are being served. > > I reset the browser using the button on the gateway page and I checked > for cookies (none found). > > I've tried it with and without the pairEndsbyName parameter. > > I've run out of things to test. > > Is there anything else that could lead to silent failures? > > Thanks > > Mike > > > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > [email protected] > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
