Answers.Body: <p>Perhaps <a href="http://genomecrispr.dkfz.de/#!/" rel="nofollow noreferrer">GenomeCRISPR</a>, 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.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-05-27T16:05:14.763Z
Answers.LastActivityDate: 2017-05-27T16:05:14.763Z
Answers.UserDisplayName: EMiller
Body: <p>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.</p>
  
  <p>I'm aware of <a href="https://www.bioconductor.org/packages/release/bioc/html/CRISPRseek.html" rel="noreferrer">CRISPRseek</a>, but I'm afraid it might be quite slow to run for a genome-scale search.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-25T22:18:42.890Z
Comments.Text: 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?
Comments.UserDisplayName: Peter Humburg
Tags: <crispr>
Title: Large-scale gRNA design for a CRISPR screen
ThreadText: # Large-scale gRNA design for a CRISPR screen
  
  (Asked by: username_0 on 2017-05-18)
  
  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](https://www.bioconductor.org/packages/release/bioc/html/CRISPRseek.html), but I'm afraid it might be quite slow to run for a genome-scale search.
  
  **Tags:** crispr
  
  > **Comments:**
  > **username_1**: 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?  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2017-05-27. Score: 2
  
  Perhaps [GenomeCRISPR](http://genomecrispr.dkfz.de/#!/), 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.
  
  
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