Is it normal to have different number of events for different samples with same index.jls?

[josegarciamanteiga]

And if so, how is then the whippet-delta treating those unique events in some samples? Thanks for the fantastic tool, Jose

[timbitz]

Hey, I don't think it's possible to have a different number of events unless you're using the --circ flag, which adds back-splice BS event entries. whippet-delta.jl ignores these, and if you filter them out there should be the same number of events from the same jls file.

[josegarciamanteiga]

Thanks! Actually I had the --circ flag! I would filter them away from my psi.gz before using them with 'GeneStructureTools' for visualization. It was giving me an error of different number of rows. I guess that's the problem. You said whippet-delta.jl ignores them...is there a way to use them for differential? I known normalization and quantification of BS events is tough but I wanted to have a look at them with whippet, too. (I am using CIRIquant in parallel). Thanks