How to perform alternative splicing from RNA Seq data?

Question

[harshraje19]

Hello everyone,

I am looking for workflow in linux or R to find out alternative splicing events from RNA-Seq data?

I am working on grapevine plants and we have 39 samples.

Can anyone suggest me tutorial or workflow for this?

Thanks in advance
Harshraj

[lieven.sterck]

what have you tried so far to get to a solution or approach?

I know for a fact that googling will give you already a clear suggestion

[harshraje19]

I am trying the leafCutter but it is not working for me. I want to know the alternate approach

Answer 1

[lieven.sterck]

I simply googled "alternative splicing in grapevine" and that got me some hits to start off with. You will for sure get a number of publications that deal with this issue, then you go look in the methods section to see what they used to find the AS events. (some examples: GUPPA, findAS, ASFinder, rMATS, cufflinks, ... )

[harshraje19]

findAS is working perfectly for me, Thank you so much