I want to compare 2 conditions: controls (4 biological replicates) v treated (3 biological replicates). I have run cufflinks successfully on all 7 BAM files independently,
I then ran cuffmerge twice to produce 2 transctipt.gtf files:
I was expecting that the two transctipts.gtf files would then be used as input (with BAM files) for cuffdiff. But, cuffdiff only allows 1 transctipts.gtf. Where have I gone wrong? Am I supposed to merge everything? Can cuffdiff tell the treated group from the control group?
Thanks in advance. Kenneth