Doubt with cryptic exon detection

[Alex Martínez Ascensión]

Hi!

I am working on a project and part of it consists of the detection of cryptic exons. I find MAJIQ very useful and the visualization in voila of the information is really helpful. However, I have some doubts about the results. I am looking for de novo cryptic exons that is, introns (or part of them) that are transcribed when they should not. However, out of the options outputted by MAJIQ, I am unsure of what to look for. Can you help me with that?

Thank you ver much

[San Jewell]

Hello,

I spoke with another modulizer user in our lab, Caleb, and he had the following suggestion to get started with your use case here:

"I would probably start with the cassette exon output, filtering for those events that have both C1_A and A_C2 flagged as de-novo AND chose some heuristics to filter for binary-like LSVs"

To be clear, he is referring to using the component "$ voila modulize" (https://biociphers.bitbucket.io/majiq-docs-academic/modulizer/how-modulizer-works.html) , and looking for the "cassette" tsv in the output directory. Please let me know if this makes any sense for your use case.

Thanks,

-San