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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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How whippet is listing alternative events? #137

Open pierreg2 opened 2 years ago

pierreg2 commented 2 years ago

Hello, I ran Whippet on two different datasets with the same annotation index but I don't have the same number of events or exons (CE) in the psi files. I'm wondering where do these differences come from? Whippet doesn't list all potential events and assign a score for each one?

Thanks Pierre

timbitz commented 1 year ago

Hi @pierreg2, Without the --circ flag, whippet-quant.jl outputs the exact same number of events (since these are nodes defined by the index) when analyzing all samples. With the --circ flag, there might be some additional lines of type BS. Every node is output, whether or not it has a PSI value assigned in that sample. Not sure how you are missing exons (CE), sounds like a mistake on your end-- the only options I can think of are that you are actually using two different indexes, or you are filtering the PSI files somehow (maybe by NA?).

pierreg2 commented 1 year ago

Thanks for your reply! I don't think that I used 2 different indexes but I'll check that. You say that filtering the PSI files by NA could be an option, how NA could be in one file and not in the other? Thanks