Alternative splicing event annotations method

Question

[Rashedul Islam]

Hi,

I am looking for a computational method to identify the number of instances of each alternative event category listed below from RNA-seq data. I tried MISO but does not give the output I wanted.

Any suggestion or link to any tool will be very helpful!

The event categories:

Skipped exons (SE)
Alternative 3’/5’ splice sites (A3SS, A5SS)
Mutually exclusive exons (MXE)
Tandem 3’ UTRs (TandemUTR)
Retained introns (RI)
Alternative first exons (AFE)
Alternative last exons (ALE)

Answer 1

[lieven.sterck]

In this publication: Exploration of alternative splicing events in ten different grapevine cultivars. , they introduced a tool called findAS , perhaps that could be of use?

[Rashedul Islam]

Thanks! I might give a try.

[Rashedul Islam]

I found this review that summarizes the tools used to find most of the alternative splicing events from RNA-seq.