Hi,

I have aligned paired-end reads to hg19 ref. genome using STAR. Before aligning, the reads were preprocessed to remove adapter sequences using Trimmomatic, and thus the reads aligned had varying lengths ranging from minimum 25 to maximum 76 nt.

I want to extract different types of AS event, for examples, cassette exon, intron retention, alt 5'/3 ss etc, from the gtf file, and quantify them between different samples.

I tried MATS and MISO tools, but both do not support reads with mixture of lengths. I don't know how to do this analysis. Could someone please suggest me some thing in this context. Any assistance is highly appreciated.