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Question: Tophat/Cufflinks Visualization
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gravatar for Alessia D
7.1 years ago by
Alessia D • 30
Alessia D • 30 wrote:
How do people on this mailing list usually visualize Tophat and/or Cufflinks results (eg. tracks on UCSC browser)? I have only this once before, and I started with a .wig file that I uploaded to the genome browser, however it looks like Tophat does not give any .wig file in the output. Suggestions? Thanks! A
rna-seq cufflinks • 2.9k views
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modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by Alessia D • 30
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gravatar for shamsher jagat
7.1 years ago by
shamsher jagat • 590
United States
shamsher jagat • 590 wrote:
Ues IGV or Galaxy tracker.
ADD COMMENT • link written 7.1 years ago by shamsher jagat • 590
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gravatar for Jennifer Hillman Jackson
7.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Alessia, Shamsher is correct, Trackster is a great choice for viewing data. The Galaxy Track Browser (aka Trackster) has several new features and more coming up in the next few weeks at the Main instance. This tutorial covers a basic RNA-seq analysis that includes visualization: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise And this wiki explains the details. One brand new feature (undocumented) allows a custom genome to be used in fasta format from your history (same basic instructions as in the wiki for a custom genome browser creation, but use the fasta file instead of a .len file). So whether your genome is native to Galaxy, or UCSC, or not, Trackster can display multiple tracks at full chromosome or zoomed view with user-defined display options: http://wiki.g2.bx.psu.edu/Learn/Visualization Hopefully this will work out for you! Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k
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