uCRISPR - Unified energetics analysis to evaluate the Cas9 on-target activity and off-target effects. Version 0.1 Author: Dong Zhang, Travis Hurst, Dongsheng Duan & Shi-Jie Chen Email: chenshi@missouri.edu Date: Feb 10, 2019
System Requirement
Linux/Unix
gcc compiler >4.8 version Compilation
Step 1. Install RNAstructure package (http://rna.urmc.rochester.edu/RNAstructure.html) Specify the location of the thermodynamic parameters before the next step (https://rna.urmc.rochester.edu/Text/Thermodynamics.html)
Step 2. Set path for DATA (line #12) and RNAstructure (line #13) in "uCRISPR.cpp" file: string DATA="[Absolute path for directory in which uCRISPR resides]/uCRISPR/data/"; string RNAstructure="[Absolute path for directory in which RNAstructure resides]/RNAstructure/exe/EnsembleEnergy"
Step 3. Make: g++ -o uCRISPR uCRISPR.cpp -std=c++11
Usage: uCRISPR [options]
Options: -h #Display help information -on file #Evaluate on-target avtivities for on-target sites in file, one site (23-mer or 30-mer sequence) per line. See "./example/OntargetSite.dat" for an example. -off file #Evaluate off-target efficiencies for off-target sites in file, one site (20-mer/23-mer wild type sequence and 23-mer off target sequence) per line in file. See "./example/OfftargetSite.dat" for an example.
Examples
a. uCRISPR -on ./example/OntargetSite.dat #Evaluate on-target sites given in file "./example/OntargetSite.dat", predicted scores are shown on the screen(Also see ./example/OntargetSite.out).
b. uCRISPR -off ./example/OfftargetSite.dat #Evaluate off-target sites given in file "./example/OfftargetSite.dat" predicted scores are shown on the screen(Also see ./example/OfftargetSite.out).