How whippet is listing alternative events?

[pierreg2]

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]

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]

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