CRISPRseek searching requirement
1
0
Entering edit mode
Daniel • 0
@daniel-9847
Last seen 7.0 years ago
US/Worcester/UMass Med

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

 

 

 

 

CRISPRSEEK • 1.1k views
ADD COMMENT
1
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 4 months ago
United States
Daniel, Thanks for the feedback! By default, only offtargets with score >= 0.5 will be in the output file. In addition, the maximum number of off targets per gRNA is set as 100 by default. Please feel free to modify min.score and topN to fit your needs, e.g., min.score = 0, topN = 1000. Best, Julie
ADD COMMENT
0
Entering edit mode

Thank you! It works now.

Daniel

ADD REPLY

Login before adding your answer.

Traffic: 730 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6