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.cuffli...@gmail.com support.
Best,
Jen
Galaxy team
On 8/10/12 12:44 AM, i b 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
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