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wenweixiong / MARVEL

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Splicing event metadata #8

Closed fpauler closed 1 year ago

fpauler commented 1 year ago

Hi, I am very interested in your pipeline and currently I am implementing it for our data. Thank you for preparing such detailed instructions, however I am running into an issue with rMATS. I am using rMATS-turbo v4.1.0 that I got from here: https://rnaseq-mats.sourceforge.net/rmats4.1.0/index.html I can run the rMATS analysis and get output files like: fromGTF.SE.txt, but I fail to find the "featureData.txt" files like SE_featureData.txt. Do you have any idea what I am doing wrong? Thank you very much for your support, best, Florian

wenweixiong commented 1 year ago

The rMATS outputs would been to be processed to match MARVEL's splicing nomenclature https://wenweixiong.github.io/Splicing_Nomenclature to generate the "featureData.txt" files. I will update MARVEL with the functions to do so in a few days time, and then I'll get in touch with you once I'm ready.

fpauler commented 1 year ago

thank you very much for your support with this issue!

wenweixiong commented 1 year ago

I have updated MARVEL by including the Proproces_rMATS function to convert rMATS splicing coordinates (fromGTF.*.txt) for MARVEL (*_featureData.txt). Demo scripts and data here: https://drive.google.com/file/d/1yv59wXhOZUmCB18VmSnOcFkmvLFURU7s/view?usp=share_link

Prior to running this function please re-install MARVEL from Github:

library(devtools) install_github("wenweixiong/MARVEL") library(MARVEL)

More info under "version 2.0.4" section of the MARLVE Github page: https://github.com/wenweixiong/MARVEL

Hope this helps :)