Question

How to perform alternative splicing from RNA Seq data?

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2.9 years ago

harshraje19 ▴ 40

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

RNA-Seq alternative-splicing • 941 views

ADD COMMENT • link updated 2.8 years ago by Ram 43k • written 2.9 years ago by harshraje19 ▴ 40

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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

ADD REPLY • link 2.9 years ago by lieven.sterck 15k

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

ADD REPLY • link 2.9 years ago by harshraje19 ▴ 40

score 2 · Answer 1 · 2021-06-30

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2.9 years ago

lieven.sterck 15k

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, ... )