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Old 11-28-2012, 02:22 PM   #24
Location: Washington, D.C.

Join Date: Jan 2010
Posts: 28


Cummerbund is the preferred option for visualizing Cuffdiff output, but it's not yet integrated into Galaxy.

However, there is a scatterplot that's handy for visualizing FPKM data for different conditions: click on the visualize icon at the bottom of a Cuffdiff expression dataset and plot column 10 (sample 1 FPKM) vs. column 14 (sample 2 FPKM). And, yes, you may want to filter for only significantly expressed genes/transcripts (using the Filtering tool).

Finally, these questions are best asked on the galaxy-user mailing list, where you can communicate with the Galaxy user community:

Good luck,
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