Question: Cuffcompare Input
0
gravatar for i b
5.3 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 • 936 views
ADD COMMENTlink modified 5.3 years ago by Jennifer Hillman Jackson23k • written 5.3 years ago by i b330
0
gravatar for Jennifer Hillman Jackson
5.3 years ago by
United States
Jennifer Hillman Jackson23k wrote:
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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENTlink written 5.3 years ago by Jennifer Hillman Jackson23k
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