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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