Hi Marcus, BAM custom track support is still under development, so it has not yet been announced or documented. We hope to release it early next year. If you are willing to take the risk of using our test server, where data and code are under active development and may not yet have been tested and approved for release, then you are welcome to try your custom tracks on the test server. In fact, I would be grateful for any feedback about the display. Here's how, if you're interested:
1. Our test server (repeat disclaimer) is genome-test.cse.ucsc.edu 2. In your custom track's "track ..." line, use type=bam and bigDataUrl=http://mysite/my.bam 3. In addition to the bigDataUrl http://mysite/my.bam, the corresponding index file http://mysite/my.bam.bai must be made accessible. 4. If your alignments are paired-end reads: * you'll need to include "pairEndsByName=." in the track line (the "." is a placeholder, can be anything) * optional but recommended: pairSearchRange=N, where N is the max expected alignment gap length, default 20000 5. If you have any problems or feature requests, contact me directly or via the genome mailing list. The track control page has several coloring options that may be useful depending on what you're looking for in the data. Thanks for your interest, Angie ----- "Marcus Breese" <[email protected]> wrote: > From: "Marcus Breese" <[email protected]> > To: [email protected] > Sent: Wednesday, December 16, 2009 11:19:35 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Custom SAM/BAM tracks > > Are BAM/SAM tracks supported on the main genome.ucsc.edu website, or > do you need to have a local version of the Genome Browser installed to > visualize BAM/SAM tracks? I found where BAM/SAM support can be > compiled in, but I've been unable to add a test BAM file as a track on > the main UCSC site. So I assume that I'll need a locally installed > version (with samtools support compiled in), but I just wanted to make > sure before I went down that road. > > Thanks for any help, > > Marcus Breese > IU School of Medicine > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
