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mckennalab / FlashFry

FlashFry: The rapid CRISPR target site characterization tool
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support for other PAM sequences #13

Open gnapham opened 4 years ago

gnapham commented 4 years ago

Is it possible to add functionality to build the off target database using custom PAM sequences?

aaronmck commented 4 years ago

Hi gnapham,

Totally; this has been requested a couple of times, I'll try to make some headway on this, though it'll take a bit of time. I'll check back when I have something here. Thanks,

Aaron

charlesfeigin commented 4 years ago

Hi, are there still plans for custom PAM sequences or alternative enzymes?

aaronmck commented 4 years ago

Hi charlesfeigin,

Slow progress on it. Right now the big issue is that we store targets in 48 bits, so we're limited to 24 basepair targets. Version 2 is in the works that will support longer target sequences. If your custom target (+ PAM) is 24 bases or less we can add support for that pretty quickly, but longer targets will require the changes in V2.

-Aaron

jdavnich commented 3 years ago

I'd just like to add my support for the custom target length (especially for Cpf1 - I'm interested in 27nt = 23 + PAM).

Very nice tool by the way.

alancleary commented 3 years ago

I'd also like to add my support for longer/custom target sequences. @aaronmck, is there an ETA on version 2?

simone-pignotti commented 1 year ago

Hi @aaronmck, any news about this feature? Thanks 🙏

sri-jumpcode commented 1 year ago

Hi @aaronmck, I have been following this issue and it would be absolutely beneficial if Flashfry could have custom PAM sites.