I would like to study alternative splicing profile of several patients.I need a tool that takes bam file as input and creates output with number of splice variants for each gene ( ex. exon skipping, intron retention, mutually exclusive, alternative 3' acceptor site...). I tried MISO but it keeps giving me error and I was not able to troubleshoot. I found rMATS easy to run but it compares two samples at a time.
Any suggestion would be appreciated!!!