Extraction of splicing events and their quantification
Hi,
I am using cuffdiff for the analysis of differential expression of isoforms and genes. I was wondering if cuffdiff offers any option to extract different types of alternative splicing events for example, exon inclusion or skip, intron retention, alt. 5' and 3' splice site selection etc, and quantify the region covering these events instead of whole isoform. I will highly appreciate if some one could guide me in this regard.
Thanks a lot.
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Anil Kesarwani
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Anil Kesarwani
1 answer
Have a look at this post: How to determine alternative splicing read counts
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Cuffdiff will provide information at the isoform level. The specific events (exon inclusion or skip, intron retention, alt. 5' and 3' site selection etc) you are talking about can be analyzed using MATS or MISO.