Hi Dave, The track and browser lines are not in the BAM/SAM file - they are entered into the "Paste URLs or data" text box on the custom track page here: http://genome.cse.ucsc.edu/cgi-bin/hgCustom. The browser line is not required; however, as it says in the BAM help page (http://genome.cse.ucsc.edu/goldenPath/help/bam.html), you *must* have a track line that, at a minimum, defines the track type and the bigDataUrl (example of full track line: track type=bam bigDataUrl=http://myorg.edu/mylab/my.sorted.bam).
You would only need to download samtools if you need to modify the BAM file, which is not needed if you are simply trying to display the data in the Genome Browser. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/21/10 5:16 AM, David A. wrote: > Hi there! > sorry for a basic question, but I am finding different kind of information > regarding this matter. I would like to load two BAM files aligned to the > mouse genome from two different samples, so around 500Mb per sample. I have > checked the BAM track format and am trying to follow the examples but I am > getting lost. > The guide says that I have to modify the BAM file in order to add browser > lines and track lines. I think that the browser lines are not necessary, but > how about the track lines? How can I modify the BAM file? Do I have to > convert it to SAM, modify it and then convert it back to BAM? > > Also, searching on the mailing list, I have found that I have to install > samtools C library. Is this necessary? > > Can I just specify the URL where these two files are stored (together with > the corresponding bam.bai files) and just press load? > > Thanks for your help, > > Dave > > _________________________________________________________________ > Hotmail: Trusted email with powerful SPAM protection. > https://signup.live.com/signup.aspx?id=60969 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
