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
•
written
by
ferris.us •
cufflinks tries to assign reads across isoforms for the same gene, but I don't recall it specifically providing information for splicing events (which I actually think are more reliable).
For the task you are describing, I think something like MATS or MISO is more appropriate:
Thanks for pointing it out! I think MISO is for quantitation. I will try MATS.
Log in to answer this question.
