mckennalab / FlashFry

FlashFry: The rapid CRISPR target site characterization tool
Other
64 stars 10 forks source link

Best Scoring Matrix for CPF1 #20

Open melkerdawy opened 3 years ago

melkerdawy commented 3 years ago

First, I would like to thank you for this amazing effort. This is by far the most convenient and complete command-line tool for Guide RNA design. I am not sure if the scoring matrices are independent of the choice of the enzyme. In other words, if I am used to the enzyme as cpf1 in indexing, can I use any of the scoring matrices (like doench2014ontarget or doench2016cfd)? My understanding is that these scoring algorithms were developed for cas9 applications so I am worried to use them with cpf1. What is your kind advice?

aaronmck commented 3 years ago

Hi melkerdawy,

Thanks for the kind words! Yeah, there are very few Cpf1/Cas12a scoring metrics out there, so you're limited to the more general off-target counts or thermostability measurements to choose guides (both doench2014ontarget or doench2016cfd won't return results for Cpf1 guides). Peter DeWeirdt was nice enough to share the scoring tables from this paper:

https://www.nature.com/articles/s41587-020-0600-6

So hopefully I can get that into FlashFry soon for those interested in Cas12a. I'll leave this ticket open until I get that chance.

melkerdawy commented 3 years ago

Hi Aaron,

Thanks for the amazing tool and quick support. This is quite rare.

Incorporating the work of Peter DeWeirdt would help many as I do not know an active command-line tool that provides that.

Just to confirm I understand you correctly. Your suggestions for the parameter to use with --scoringMetrics if I am scoring cpf1 quides will be dangerous, minot, folding. Anything else do you think I should add?

Thanks a lot

aaronmck commented 3 years ago

Yeah I think that's it for now; I'll keep this issue open as I hope to get the Cpf1 scoring in over the holidays. Thanks!

-Aaron

maximilianh commented 3 years ago

Great to see this. I'm also interested in this for crispor.org...

On Thu, Dec 10, 2020 at 8:37 PM Aaron McKenna notifications@github.com wrote:

Yeah I think that's it for now; I'll keep this issue open as I hope to get the Cpf1 scoring in over the holidays. Thanks!

-Aaron

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mckennalab/FlashFry/issues/20#issuecomment-742748776, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TLCVEWHCF26A6XGFKLSUEPQXANCNFSM4USUD43Q .