Identify Alternative Splicing Event using exon and junction count table

Question

[rhonddaskl]

Hi folks,

I'm trying to identify alternative splicing events using the junction count table and exon count table generated by STAR, as well as the feature count obtained from RNA-seq data. The example dataset is shown below. I was wondering if it is possible to identify five types of alternative splicing events based solely on these two files. if so, is there a tool can be used for such a task?

Thanks!!!

Junction Count Table:

Exon Count Table:

[Buffo]

I think you're referring to the SJ.out.tab, aren't you? In that case, it summarizes the SJs and their coverage. To analyze splicing variants you need to perform the assembly first since a SJ doesn't necessarily produce an transcript. A transcript assembler such as StringTie can do the job.

[benformatics]

You're better off just using your STAR index with a pre-existing tool. Try rMATS: https://rnaseq-mats.sourceforge.net/faq.html#5

[Eric Lim]

If you don't need splicing events not annotated in a GTF, you can use SUPPA2 (https://github.com/comprna/SUPPA). You'd need transcript expression, ideally in TPM.

[Ram]

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.