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Extracting sequence from the output of rMATS #378

Open arafmahmud opened 6 months ago

arafmahmud commented 6 months ago

Hello,

Is there a way to get the sequences of the isoforms after the rMATS analysis? I am trying to use rMATS to identify the sequences that has been changed due to alternative splicing. Is there a way to get the sequence that has alternative splicing related changes from the tabular output?

Thanks for the support.

EricKutschera commented 6 months ago

The rMATS output files include coordinates for the events. You can use those coordinates to look up the sequence in the reference fasta. Here's a related post about using rMATS coordinates: https://github.com/Xinglab/rmats-turbo/issues/371

arafmahmud commented 6 months ago

Are there any tools or scripts available to do that using the output?