Question: Cuffcompare Input
gravatar for i b
5.7 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 • 1.1k views
ADD COMMENTlink modified 5.7 years ago by Jennifer Hillman Jackson25k • written 5.7 years ago by i b330
gravatar for Jennifer Hillman Jackson
5.7 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 5.7 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 90 users visited in the last hour