Voila modulize module_event_combination interpretation

[d bogdanoff]

Hello, 

Thanks for developing and maintaining MAJIQ. I've been running the voila modulize tool to annotate splice junctions into different event type groups (cassette, alt3'/5', etc) for specific downstream analyses. To this point, I've been using the individual event type .tsv files output by voila modulize, but would like to use the junctions.tsv file to access the classifications of all types in a single process. Would you be able to help with my interpretation of the module_event_combination column in the junctions files? For example, in the value:

cassette^3|ale^11|afe^3|multi_exon_spanning^4

How are the caret/superscripted numbers following the event type to be interpreted? I assumed they were some sort of ranking of the sub-events within a complex splicing structure - some clarification here would be much appreciated. Let me know if I can provide any clarification myself regarding the question. 

Thanks again, 

Derek

[San Jewell]

Hello Derek,

I would check out the page https://biociphers.bitbucket.io/majiq-docs-academic/modulizer/how-modulizer-works.html for a good overview.

Basically, this looks like a case where there's a very complex module detected with the thresholds set (large area between single entry/single exit) , and inside that area there are three possible cassettes, 11 alternate last exons, 3 alternate first exons, and 4 cases of multi exon spanning.

Perhaps you can run voila view on this data to get a clearer picture of what this large module looks like?

Let me know if it makes sense.

Thanks!

-San