After reading the doc and doing many tries (and fail) I was wondering if there is a way to force majiq deltapsi to use one specific condition as the control, and the other as a test.
If I'm correct, a negative deltapsi is supposed to show (for exon skipping for example) that the exon is mainly excluded in one condition comparing to the other. My problem is that, I have values that are the opposite of what they are supposed to be : sometimes I have a negative deltapsi, but in bio experiments, it shows that it should be positive.
I have two conditions T5 and unT5. When I do the majiq deltapsi I want the deltapsi to be calculated as unT5 is the control and T5 is the test so the deltapsi should be calculated like : T5 E(PSI) - unT5 E(PSI)
But this is not the case.
I tried to set the test condition as the first group in the majiq delta psi such as (short example) :
majiq deltapsi -grp1 T5_1.majiq T5_2.majiq T5_3.majiq -grp2 unT5_1.majiq unT5_2.majiq unT5_3.majiq -n T5 unT5
I don't understand how am I supposed to do.
Thanks a lot for reading me,