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Question: Cuffcompare Input
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gravatar for i b
6.1 years ago by
i b • 330
i b • 330 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
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modified 6.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.1 years ago by i b • 330
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gravatar for Jennifer Hillman Jackson
6.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 6.1 years ago by Jennifer Hillman Jackson ♦ 25k
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