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Question: Cuffcompare Inputs
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gravatar for i b
6.3 years ago by
i b • 330
i b • 330 wrote:
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
rna-seq cuffdiff • 1.3k views
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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by i b • 330
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gravatar for Jennifer Hillman Jackson
6.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Irene, Yes, if using CuffDiff with a reference GTF file, all inputs must in present. One way to create this GTF is using CuffCompare. Our example protocol is to run CuffMerge (which runs CuffCompare as part of the process) with all inputs prior to running CuffDiff. The updated RNA-seq tutorial covers the details: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise The Cufflinks website has some sample protocols where CuffCompare is used alone (without proceeding to CuffDiff). http://cufflinks.cbcb.umd.edu/tutorial.html#discovery I know that we have pointed there before, but it really is the best resource (what the content on Galaxy is based on), along with the primary paper and tophat.cufflinks@gmail.com support. Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k
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