Tools to Study Intronic Regions from RNA-Seq Data

Question

[Aynur]

Hello, I performed DEG analysis from mouse RNA-Seq. However, as I have around10% intronic mapping, I want to study this intronic region and get some biological meaning. I tried to do literature search , but could not find any relevant articles or tools. I hope experts suggest me some articles and tools to study this intronic regions. Any advice is appreciated. Thanks for reading my post. Below is the mapping result for your reference.

Answer 1

[GouthamAtla]

Probably those intronic reads are coming from unannotated exon or via an intron retention event. Did you check the bam file how the data looks and which introns ? You could simply get the intron coordinates (leafcutter) and identify introns from which those reads are coming from (featurecounts).

You can use MATS or MAJIQ to quantify the intron retention events and perform differential analysis.

[Aynur]

Thank you very much. I did not check Bam files, but I just used STAR Aligner to align to genome and then got these mapping result. I will check out leafcutter to identify intronic regions. Do you think it is worth looking into intronic regions ? or am I supposed to ignore it as I have high exon readings.

[GouthamAtla]

By examining the intronic reads, you are evaluating if there is any unannotated coding exon that might be deferentially expressed. Or if you quantify intron retention events, you are evaluating alternative splicing differences. Both are biologically interesting, but it will be a lot of work.