How to interpret complexity column in the .psi.gz output files?

[MorticiaGiulia]

Hello all, I have two questions about the complexity column in the .psi.gz output files I hope to seek help from you. 1) Are the values in this column a prediction of the complexity of the relevant node or a report of actually observed complexity of this node in the RNA-seq sample I'm analyzing? 2) Does a K0 mean this node is constitutive in the particular RNA-seq sample I'm analyzing or based on initial files used for building the index? My apologies in advance if any questions are unclear, which I can further clarify. Thank you for your time!

[timbitz]

Hi @MorticiaGiulia-- (1) Yes, the values are a report of the actual observed complexity of this node in the RNA-seq sample you're analyzing. (2) K0 means the node is constitutively included or excluded in the sample your analyzing. Whippet allows alternative splicing across any exon-exon junction or splice-site, regardless of whether there is evidence of alternative splicing in the annotation used for building the index. So it doesn't rely on the index for that, just for the node boundaries. Everything else reported is what it observes in the sample.