Hi guys,
a bit of confusion about how to give cuffdiff certain outputs:
having 1 control and 8 tumour samples which I consider biological
replicates (not technical replicates), how shall give the input to

If I want to use cuffcompare as gtf: shall I cuffcompare all 8samples
plus the control and then run cuffdiff using this gtf?
When adding the bam files, shall I have to make 8 groups plus control groups?
or one groups with 8 bams and second group with the control bam?

Much appreciated an answer!!

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