Cufflinks/Cuffdiff Multiple conditions

Question

[Raygozak]

Hi, I can see that in the CummerBund tutorial they have more than two conditions being contrasted, I'm used to doing everything pairwise even when calling cuffdif/cufflinks. How can I make many (perhaps pairwise) comparisons in a single command line call of the Cufflinks pipeline?

Thanks

Answer 1

[Sukhi Singh]

Why do you want to do it?

Consider three conditions, A,B,C.

When you run cuffdiff, it will do all the pairwise comparisons automatically, A-B, B-C, A-C so you don't have to do it manually.

CummerBund contains the tools to plot pairwise data or you can also make custom codes to process gene_exp.diff file, if you are just interested in DEGs. I would recommend running cufflinks/cuffdiff with all the replicates you have, the resultant file is just longer, it will contains all the comparisons that you'd do one by one.