Is there any software available to count the splice junction reads for each junction? Specifically, I would like to count 1) exon-exon splicing reads, 2) exon-intron spanning reads for ALL JUNCTION SITES.
Considering alternative splicing events, I would also like to count exon-exon junction reads at each junction site for all exon-exon pairs.
I read on papers and see people do that, but I cann't come up with a easy way to do it. I would be good if anyone can suggest any software or ideas.