We are comparing two RNA-seq datasets (read length = 150nt, depth = 50M reads, 2 conditions, n = 4 per condition) for alternative splicing. I used rMATS and altanalyze to find alternative splicing events. However, there is very little overlap between the results.
This paper says that there wasn't much overlap between rMATS and SUPPA in their study. https://www.nature.com/articles/s41467-020-15815-7#Sec15
We plan on experimentally validating some of the top hits using qPCR. Which results should we use? Are they both correct? Is this due to my error in running rMATS?