Hi all. I have 24 samples RNA-seq, paired-end data including 2 genotypes, 3 Zone from root, 2 conditions and each condition including two replicate. How can I do cuffdiff for this expriments. thanks alot
Unfortunately you cannot analyse your experimental setup with Cuffdiff as it cannot handle overlapping conditions/co-factors. For this you need to use cuffquant and cuffnorm (see overview here) to get a count matrix which you can then analyze with DESeq2, edgeR or similar.