Hello Irene,

Yes, if using CuffDiff with a reference GTF file, all inputs must in present. One way to create this GTF is using CuffCompare.


Our example protocol is to run CuffMerge (which runs CuffCompare as part of the process) with all inputs prior to running CuffDiff. The updated RNA-seq tutorial covers the details:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

The Cufflinks website has some sample protocols where CuffCompare is used alone (without proceeding to CuffDiff).
http://cufflinks.cbcb.umd.edu/tutorial.html#discovery
I know that we have pointed there before, but it really is the best resource (what the content on Galaxy is based on), along with the primary paper and tophat.cuffli...@gmail.com support.

Best,

Jen
Galaxy team

On 8/10/12 12:44 AM, i b wrote:
Dear all,
given 3 samples, 1 control and 2 treated replicates when I do
cuffcompare to produce the gtf input for cuffdiff, do I have to run it
with or without the cufflink control?
E.g. Cuffcompare with only my 2 treated replicates?--------------use
this gtf to run cuffdiff
        Cuffcompare 1 contro and 2 treated replicates?--------------use
this gtf to run cuffdff

Thanks a lot
ib
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