Question: Detect Alternative Splicing Events And Count Them From Cufflinks Results
2
gravatar for ferris.us
6.7 years ago by
ferris.us20
ferris.us20 wrote:

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

splicing exon • 2.4k views
ADD COMMENTlink modified 6.7 years ago by Devon Ryan97k • written 6.7 years ago by ferris.us20
3
gravatar for Charles Warden
6.7 years ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

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/

ADD COMMENTlink written 6.7 years ago by Charles Warden7.9k

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

ADD REPLYlink written 6.7 years ago by ferris.us20
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