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evaluate single end RNA-Seq data results #353

Open Qingru44004 opened 8 months ago

Qingru44004 commented 8 months ago

Hi,

Right now, I only have the single-end RNA-Seq for the disease and control samples I am studying. I am wondering if there is a good way to evaluate whether the single-end results are acceptable, how comprehensive it is, and whether it is suitable to use rMats in my case? Do you have any suggestions? Thanks!

EricKutschera commented 8 months ago

Single-end data is fine for rMATS. With paired-end data, rMATS just filters out alignments that don't have the proper pair flag: https://github.com/Xinglab/rmats-turbo/issues/153