My purpose is to detect alternative splicing events and count them. Someone mentioned tophat->cufflinks. But I don't know how to use the result generated by cufflinks to create a statistic table likes below. Any ideas? Thanks!
Intron Retention : 2,465 (26.9%)
Skipped Exon : 2,026 (22.1%)
Alt. 5' : 2,922 (31.8%)
Alt. 3' : 1,763 (19.2%)
Total : 9,176