Here is a description of the parameter useEfficacyFromInputSeq.
Default FALSE. If set to TRUE, summary file will contain gRNA efficacy calculated from input sequences instead of from off-target analysis. Set it to TRUE if the input sequence is from a different species than the one used for off-target analysis.
FYI, you can find this information by typing the following command in a R session.
Efficacy score is calculated according to the following paper regardless of the value of useEfficacyFromInputSeq.
Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol. 2014 Sep 3. doi: 10.1038 nbt.3026
BTW, CFDscore method used for offtarget score prediction is from the following paper.
Doench JG et al., Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology Jan 18th 2016
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Subject: [bioc] CRISPRseek gRNA efficacy
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User joyce<https: support.bioconductor.org="" u="" 14189=""/> wrote Question: CRISPRseek gRNA efficacy <https: support.bioconductor.org="" p="" 102403=""/> :
I noticed an option, "useEfficacyFromInputSeq", in offTargetAnalysis. Could you please explain how the gRNA efficacy is calculated from off-target analysis, and how is it different from the one calculated from the input sequence? Does either correspond to the Rule Set 2 scoring methods in Doench, Fusi et al., Nature Biotechnology 2016<http: www.nature.com="" nbt="" journal="" vaop="" ncurrent="" full="" nbt.3437.html="">?
Thank you very much for your help.
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