text: user182: 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.
  
  user33: 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.
  
original_text: 182: <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>
   33: <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>
  