Best Scoring Matrix for CPF1

[melkerdawy]

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]

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]

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]

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]

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

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On Thu, Dec 10, 2020 at 8:37 PM Aaron McKenna ***@***.***> 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 <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACL4TLCVEWHCF26A6XGFKLSUEPQXANCNFSM4USUD43Q> .