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
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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