Hi Eric,

UCSC has many details on their web site about how to customize color coding in BAM data, please see:


http://genome.ucsc.edu/goldenPath/help/bam.html
http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html

The Text Manipulation tools in Galaxy may be helpful for certain steps and the track controls at UCSC for others. If you have questions, asking them directly at gen...@soe.ucsc.edu would be the best advice (sometimes they also reply to this mailing list, so we can watch for that). Or, you can search their mailing list archives to see if the topic has been brought up before: http://genome.ucsc.edu/contacts.html

Best wishes for your project,

Jen
Galaxy team

On 1/5/12 3:18 PM, Eric Guo wrote:
Hi all,

I have two small RNA libraries that are biological replicates. I mapped
the reads onto the genome using Bowtie and displayed the BAM files as
two individual tracks on the UCSC genome browser. However, this is not
very nice.

Ideally, I would like to color the reads from each library with a
different color, so that I could display them in the SAME track. Because
the two replicates are color labeled, I would be able to tell which
experiment a particular read comes from.

I have two BAM files from each library. All I need to do is to label
them with different colors, then merge them before displaying on genome
browser.

Does anyone know how to do this?

Thanks in advance for your help!

-Eric


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___________________________________________________________
The Galaxy User list should be used for the discussion of
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