How does the insert size parameter change after trimming (MATS tool)

Question

[Anil Kesarwani]

Hi,

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.

[Anil Kesarwani]

Many thanks for your answer

Answer 1

[Istvan Albert]

The insert size is not (should not) be affected by trimming.

The insert size refers to the lengths of the sequences in the DNA library submitted to sequencing.

That being said the above assumes that you are trimming off sequences that are actually incorrect (adapters, errors etc).

If you were to trim off a fixed number of bases from all correct reads as well then the net effect is similar to having sequenced a library with a shorter insert size.

[Anil Kesarwani]

I used Picard to calculate the average length of reads and standard deviation in each sample, which seem to be critical parameters for MATS