How VOILA categorizer works
Purpose: focus on just the biologically relevant junctions and exons in the splicegraph.
After decomplexifying (e.g. here, usingdecomplexify reads thresholdof 200):
This should look familiar (see: MAJIQ Build simplifier). A critical difference, however, is that the MAJIQ Build simplifier removes junctions from the splicegraph before the MAJIQ Quantifier. Thus, the MAJIQ Build simplifier affects estimates of PSI. The VOILA categorizer, however, operates downstream and independently of the MAJIQ Build, so since this decomplexifier stage simply ignores irrelevant junctions; junction PSI estimates from the input VOILA files are not altered.
Note: by default, junctions that are retained have PSI>=0.05 in any one of the input voila files. Decomplexify by default also removes junctions with 0 reads. See decomplexify stage arguments for more options and details.
Modules in general have a single entry where there is a split splicing decision, and a single exit. However, alternate starts and ends of transcripts may also be modules (see example).
These modules are simple binary cassette exon events. See other examples with more complicated modules and events here.