I was using rMATS to do alternative splicing analysis.
My command is like this:
python $rMATS/rmats.py --b1 ko.txt --b2 wt.txt --gtf ./GCF_000001405.39_GRCh38.p13_genomic.gtf --od ./rMATS -t paired --readLength 150 --cstat 0.0001 --nthread 1 --libType fr-secondstrand
It keeps running but no outputs nor any errors reported.
I searched to try to find an answer and found this. I checked and believed the indexes being used are okay.
Does anyone know how to solve this? Or does rMATS doesn't give outputs until it finishes all its processes? Thank you.