Identify Alternative Splicing Event using exon and junction count table
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:
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rhonddaskl •
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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.
You're better off just using your STAR index with a pre-existing tool. Try rMATS: https://rnaseq-mats.sourceforge.net/faq.html#5
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.