Hello, Yes, this has not changed. The reference GTF given to Cuffdiff must contain all of the transcripts of the inputs: http://user.list.galaxyproject.org/cuffcompare-inputs-td4654384.html Run this as you have done previously: http://user.list.galaxyproject.org/cuffcompare-outputs-missing-td4654259.htm... Some other useful advice quoted directly from the tool author: http://user.list.galaxyproject.org/Re-1-cuffcompare-or-cuffmerge-td4581029.h... Hopefully this helps! Jen Galaxy team On 10/17/12 12:34 PM, i b wrote:

dear forum, I have two samples, treated and untreated. When I run cuffcompare (to created the gtf file for cuffdiff) do i have to give as input the cufflinks from both samples and the reference annotation or only the treated cuffliks?

I very confused. any help much appreciated.

thanks, ib ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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