I was wondering if there is any tool to calculate PSI from the BAM files. Basically what I want is-
I have gtf file with all the exons and I want to calculate for each exon (lets take exon filled with grey for example) how many reads mapped to junction of that exon (a and b in figure) and how many reads skip that exon (c in figure). So if we have, let's say, 10k exons in the gtf, the output should contain 10k rows with a,b and c as columns.
I used MATS and bam2ssj but did not get what I was expecting. I have gtf file with approx. 300k exons but MATS gives the output only for 3k exons. bam2ssj is calculating the values for introns rather than exons.
Thanks in advance.