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
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
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