QUESTION: How to integrate netchop results to aditionnally filter possible peptides

[PierreLaplante]

Hello, I would like to know your current take on integrating the clivage score in the pipeline.
I ran the downstream filtering from the all_epitopes.tsv myself, and wanted to see results from NetChop with the predicted neoantigens.
With my current experiment, it seems that most of the PASS neoantigens I obtained running the pipeline report an internal clivage site above 0.5.
It seems inacurate to just discard them all, so I wanted to know how you implemented this score in the pipeline as downstream filtering.
Thank you.