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Question: Default Display Replicate Libraries With Different Colors
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gravatar for Eric Guo
6.9 years ago by
Eric Guo • 60
Eric Guo • 60 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 
alignment bowtie • 847 views
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modified 6.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.9 years ago by Eric Guo • 60
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gravatar for Jennifer Hillman Jackson
6.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 genome@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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 6.9 years ago by Jennifer Hillman Jackson ♦ 25k
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