Can any RNA-Seq reads be analyzed using rMATS?

[Sahu-Mousumi]

Hi!

I have rRNA depleted total RNA-Seq reads obtained using below kits. Can I use these to identify all AS events? (I am getting SEs and MXEs and no other as events using rMATS.) Is there any specification for RNA-Seq type for AS analysis?

RNA-Seq kit- Total RNA was extracted using PAXgene Blood RNA Kit. Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

Thank you, Mousumi

[EricKutschera]

Here is a post about getting only SE and MXE events: https://github.com/Xinglab/rmats-turbo/issues/327

You could try running with --novelSS to let rMATS look for more events.

rMATS will print a section of output that says how many reads it used and how many were filtered out for different reasons. The section in the output starts with read outcome totals across all BAMs. The post linked above has an example