Definition of junction categories in compendium_cryptics

[Tomas-Solomon]

Hi everyone,
I am working with compendium_cryptics and was wondering if there is documentation or a brief explanation available for the junction categories none, ambig_gene, and novel_combo. Any insights on what these represent would be much appreciated.

[aleighbrown]

Hi there!

We use a modified form of a function from the dasper package to re-annote MAJIQ splice junctions.
https://dzhang32.github.io/dasper/reference/junction_process.html

none - Neither end of the junction lies on a known splice site according to the GTF
ambig_gene - junction ends couldn't be cleanly resolved to known genes
novel_combo - known exons, novel combination of them according to the GTF annotation

I'll make sure to add this information into the revision of the manuscript methods.

In practice, I find the novel_donor/acceptors tend to the be the most intuitive, whereas the none are typically in my experience novel 3'utr splicing events.