Question: No output from Cuffdiff
gravatar for maggiecrow
4.5 years ago by
maggiecrow0 wrote:


I've been running Cuffdiff on Galaxy today, exactly as I did last week (using the same reference transcriptome, bam files, the same parameter settings, on the same version) however I am getting nothing out. Cuffdiff is reporting "no test" for every gene/transcript.

Has a change been implemented to the tool that is making it non-functional? Any help would be greatly appreciated.



Tool name: Cuffdiff
Tool version: 0.0.7
Tool ID:
ToolShed URL:


cuffdiff • 1.3k views
ADD COMMENTlink modified 4.5 years ago by Jennifer Hillman Jackson25k • written 4.5 years ago by maggiecrow0
gravatar for Jennifer Hillman Jackson
4.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Maggie, 

This is occurring on The server has been updated in preparation for the upcoming release. Would you be able to share this history with me? There are some known items we are working through, but whether this is related or not I'd very much like to confirm. Share by emailing me a share link (to maintain your data privacy) - this is the first option on the Share form under the history menu "Share or Publish", and send it to:

How to share:

If you happen to have the original successful run in the history, please leave it there. Also please be sure that all inputs back through fastq upload are present.

Thanks for reporting the issue! Jen, Galaxy team

-- Update --

Hi Maggie - did you close this? If this is the same history as you reported a bug for later yesterday, then the Cuffdiff results from the new run (deleted) appear to be the same as the original runs. From a quick look, it appears that the option to summarize by read groups was selected, but read groups are not present in the inputs. Try running without this option, or add read groups to your inputs with the Picard tool. If you need more help, let us know. Jen

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Jennifer Hillman Jackson25k

The author of a post or moderators may close/delete a posts (using the moderate link) but only moderators can reopen them.

It occasionally happens that a user accidentally deletes their own post but then they cannot reopen it nor will they be able to see the post. I usually reopen the post and ask them the close it instead of deleting.

Another type of situation occurs when users think that an answered post is now solved therefore should be deleted. In that case the post should be tagged as accepted by the author instead of being deleted.

ADD REPLYlink written 4.5 years ago by Istvan Albert250
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