I have a question regarding read lengths in MATS tool. I aligned adapter-trimmed paired-end reads using STAR, and used sorted bam files as input to MATS for the analysis of splicing events. Originally, each mate length was 76, but after trimming it can be of any length. Given, I provide average insert length (r1 and r2) and the corresponding sd1 and sd2 values to MATS, does the read length should still need be same in different samples and replicates. If this is so, why MATS requires r1,r2 and sd1,sd2.
Please help me out understanding the above problem.