I am new to RNA-Seq analysis and am struggling a bit with setting up the CuffDiff
I have two conditions and for each I have 3 replicates. I want to compare significantly different expression between conditions but also between replicates within conditions.
Can I run this all at once and if so how?
I get the impression that I need to run CuffMerge first to put all 6 datasets together into one file but after running this with the two conditions (containing 6 datasets each), there seems to be no distinction between replicates.
Should I run the 6 'assembled transcripts' files from Cufflinks separately against all three replicates of each condition? That seems to lead to many files.
Hope that makes sense!