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.html

Some other useful advice quoted directly from the tool author:
http://user.list.galaxyproject.org/Re-1-cuffcompare-or-cuffmerge-td4581029.html

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
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Jennifer Jackson
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