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Question: Galaxy Cuffdiff output doesnt correspont the output from manual
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gravatar for Wanderer
11 months ago by
Wanderer • 10
Wanderer • 10 wrote:

Hi people! I was trying to run the local version of cummeRbund but the files that I get from the cuffdiff output from galaxy werent the same extension, the manual from cummeRbund says that cuffdiff outputs are those files:

isoforms.fpkm_tracking genes.fpkm_tracking cds.fpkm_tracking tss_groups.fpkm_tracking

isoform exp.diff gene exp.diff tss group exp.diff cds exp.diff splicing.diff CDS.diff promoters.diff

I tried to change the extension of the files to try to run the readCufflinks() to create the database to visualize the results but wasnt possible, anyone has a hint?

I already tried to use the cummeRbund from galaxy but isnt working, I cant create expression and volcano plots.

Thanks so much!

@jennifer Thanks!!!
rna-seq galaxy cuffdiff • 344 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by Wanderer • 10
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gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the CummeRbund tool wrapped for Galaxy has known issues with the plotting functions. The issue involves the content of the outputs produced by Cuffdiff for CummeRbund, so using the data outside of Galaxy is also going to be problematic right now.

The issue is tracked here and a fix is still in progress: https://github.com/galaxyproject/tools-devteam/issues/340

Thanks! Jen, Galaxy team
ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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