Hi Julie, I have read a paper titled "Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens",and have found one approach described is interesting for design the sgRNA. Basically, they first select the exonic guide sites fitting the pattern G(N16–19)NGG, and then annotate these guide sites as targeting Ensembl GRCh37 genes models to generate candidate guides towards each gene. could we use CRISPRseek for this purpose. Thanks, Xin

Hi Xin,

Yes, you can use CRISPRseek to find gRNAs with the pattern of G(N16-19)NGG with the input Exon sequences. You will need to call the function offTargetAnalysis 4 times, i.e., set gRNA.size = 20, gRNA.size = 19, gRNA.size = 18, or gRNA.size = 17 each time. In addition, you will also need to set gRNA.pattern = "^G".

Please note that the paper did mention about offtarget analysis as well.

Best regards, Julie