Detect Alternative Splicing Events And Count Them From Cufflinks Results

Question

[ferris.us]

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

Answer 1

[Charles Warden]

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:

http://rnaseq-mats.sourceforge.net/

http://genes.mit.edu/burgelab/miso/

[ferris.us]

Thanks for pointing it out! I think MISO is for quantitation. I will try MATS.