Question: Cuffcompare Input
gravatar for i b
6.1 years ago by
i b330
i b330 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
rna-seq cufflinks • 1.2k views
ADD COMMENTlink modified 6.1 years ago by Jennifer Hillman Jackson25k • written 6.1 years ago by i b330
gravatar for Jennifer Hillman Jackson
6.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello, Yes, this has not changed. The reference GTF given to Cuffdiff must contain all of the transcripts of the inputs: Run this as you have done previously: td4654259.html Some other useful advice quoted directly from the tool author: td4581029.html Hopefully this helps! Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.1 years ago by Jennifer Hillman Jackson25k
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