Question

Rna-Seq Analysis

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12.3 years ago

KS ▴ 380

Hello everyone,

I am analyzing RNA-Seq data paired end data using galaxy. I did the QC and I ran TopHat on the data.

TopHat produced 4 output files and I am not sure how to visualize or analyze those files. The data I am analyzing is prostate cancer data and I want to look for a specific splice variant which is TMPRSS2-ERG genes.

It would be great if anyone can guide me in steps in visualizing the TopHat output on galaxy

tophat galaxy rna-seq analysis • 3.2k views

ADD COMMENT • link updated 12.3 years ago by lythimus • 0 • written 12.3 years ago by KS ▴ 380

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I haven't worked with galaxy. But as an alternative, how about saving the mapped bam files on your computer/cluster and visualizing with IGV?

ADD REPLY • link 12.3 years ago by Arun 2.4k

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Some material which might help you. DE with splice variant analysis and galaxy test RNA-Seq workflow.

ADD REPLY • link 12.3 years ago by Sukhi Singh 11k

score 0 · Answer 1 · 2012-08-02

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12.3 years ago

Ido Tamir 5.2k

You could visualize it in galaxys own browser "trackster". There should be an icon like a line chart in the dataset. Click it and follow the instructions.

ADD COMMENT • link 12.3 years ago by Ido Tamir 5.2k

score 0 · Answer 2 · 2012-08-03

Galaxy is extensible and open. Meaning if you want to keep your data within the Galaxy framework you can run your own instance of it and create or download (likely from the Galaxy Tool Shed) your own tool to process the data with whatever software you desire. Alternatively, as Arun suggested, you can export your data and analyze it outside of the Galaxy framework.