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?
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written
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GouthamAtla
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.
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.
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written
by
GouthamAtla
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