10
$\begingroup$

What are the best tools to design gRNAs in a high-throughput way for a CRISPR screen, e.g. targeting all protein-coding genes in a genome? I would like to take into account possible off-target effects, as well as to allow for flexibility in the PAM sequence, to have the possibility of using non-canonical PAMs.

I'm aware of CRISPRseek, but I'm afraid it might be quite slow to run for a genome-scale search.

Improve this question
$\endgroup$
1
  • 2
    $\begingroup$ I don't have enough experience with CRISPR to give a useful answer. I have one observation though. You say that you are afraid that CRISPRseek might be quite slow for a genome-scale search. Have you actually tried? It sounds like this problem should parallelize well. Presumably, you could run one gene at a time, running as many in parallel as your resources allow? $\endgroup$
    – Peter Humburg
    May 25, 2017 at 22:18

1 Answer 1

Reset to default
2
+50
$\begingroup$

Perhaps GenomeCRISPR, I've personally never used it, but it has a well-documented API and appears you could automate it to go through the whole genome.

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.