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.