Is there anyway to manually define the CEG and NEG files for bagel. Our library doesn't include the same genes and this causes the pipeline to fail?

Hi Andrew, I don't have access to my computer right now but yes it should be in the do normally

Thanks

Hi sorry, getting back a bit late to you but it’s

--bagel_reference_essentials

and

--bagel_reference_nonessentials

Thanks. That’s really helpful.