Hi Julie,

I have used CRISPRseek to predict off-target sites of Nme guide RNAs. One thing I have observed is that for some guides CRISPRseek showed same off-target sites with mismatches less than 6 even though I reset max.mismatches = 8. Some criteria I missed? Script is attached below.

Results2 <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, gRNA.size = 24, findPairedgRNAOnly = FALSE, BSgenomeName = Hsapiens, chromToSearch = "all",  PAM = "NNNNGATT", PAM.size=8, PAM.pattern="NNNNGNNN$",weights = c(0,0,0,0,0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583), txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 8, outputDir = outputDir, allowed.mismatch.PAM = 7,overwrite = TRUE)

Thank you!

Daniel