I am interested in the study of alternative splicing sites 5 and 3 and Intron retenton. I just want it, in the form of read count that how many numbers of reads and percentage of reads/total coverage reads, belongs to one splice site and same thing for other site.
NOTE: I don't have two different conditions.(so i am not considering MATS and related tools)
I aligned reads to reference using STAR and I have STAR out.tab file with unannotated and annotated events. Now, How I can extract information like listed below for 5',3' SS and IR events.
example [5' SS]:
start end number_of_reads chr1 10300 10500 40 chr1 10350 10500 150