I am using rMATS (version 4.0.2) to test for alternate splicing. I have 12 paired samples (12 replicates for normal and 12 replicates for diseased). Sample 1 (Normal) is paired with Sample 2 (Diseased) Sample 3 (Normal) is paired with Sample 4 (Diseased) ..and so on
It is mentioned that rMATS can test for both paired and unpaired replicates. However I do not find any options in rmats.py script to specify whether replicates are paired or unpaired. The only option I find is to create 2 lists, one for each condition, separated by comma.
So my list (for Normal) goes as sample1, sample3, sample5.. and my list (for Disease) goes as sample2, sample4, sample6..
How does rMATS know whether to test for paired replicates in this case?