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mckennalab / FlashFry

FlashFry: The rapid CRISPR target site characterization tool
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Filtering gRNAs for GC% and homopolymers #33

Open sri-jumpcode opened 2 years ago

sri-jumpcode commented 2 years ago

Hi Aaron:

Been using FlashFry for quite a few years now. In my current project, I am designing millions of gRNAs and before we synthesize them, we filter the gRNAs based on GC% and homopolymeric sequences in the guide target. Is there anyway you can add as an optional filter these parameters?

aaronmck commented 2 years ago

Hi @sri-jumpcode,

Do you mean a filtering option before scoring at the discovery phase? Right now if you set the -numericOutput for scoring it will give you the raw numbers for GC which could be helpful too.

sri-jumpcode commented 2 years ago

I was thinking more during the process of discover. If guides have Gc% above or below a threshold, the discover step could automatically reject that guide.

aaronmck commented 2 years ago

I added the GC filtering to the newest 1.15 release. It'll take a little longer on the homopolymer run as I don't have something baked in for that yet.

sri-jumpcode commented 2 years ago

Thanks Aaron, will test it today and let you know. Again, really great work!!!