cuffdiff2 options regarding replicates ?

Question

[GouthamAtla]

Hi, I am using latest version of cuffdiff. I would to what is the meaning of this option in cuffdiff2

--min-reps-for-js-test       Replicates needed for relative isoform shift testing  

Does it mean the number of replicates needed to perform differential isoform analysis ? Because I have two replicates for one condition and 3 for another condition.

Should I change the default value from 3 to 2?

Answer 1

[iraun]

Yes, in your case you should change the value from 3 to 2.

--min-reps-for-js-test argument refers to the minimum number of replicates for each sample in your experiment, so, if you have some samples with 3 rep, and some other with 2, you should specify --min-reps-for-js-test 2, otherwise, if you put 3, the samples with 2 replicates won't be analyzed.

[GouthamAtla]

The results are same with --min-reps-for-js-test 2 or --min-reps-for-js-test 3. I got same number of differential Genes/Isoforms with exactly same values.