CASPER Off-Target Algorithm

This algorithm uses CASPER's indexes from Seq-Finder to find and score potential off-target sites for input gRNAs.

Download And Compile Sqlite3

Linux:

1. Open terminal
2. Run the following command: sudo apt-get install sqlite3

Mac and Linux (if you did not use apt-get):

1. Download sqlite3 source code
2. Open terminal
3. CD to sqlite3 source code folder
4. Build using the following command: gcc -c sqlite3.c
   • The build command should generate a .o file that will be used with compiling OT.
5. Copy the .o file to the OT source code folder

Windows (Visual Studio 2017):

1. Download sqlite3 source code
2. Open "Developer Command Prompt for VS 2017"
3. CD to sqlite3 source code folder
4. Build the library files by running the following command: lib /DEF:sqlite3.def /OUT:sqlite3.lib /MACHINE:x64

Download and Compile OT

Linux (if you used apt-get install sqlite3):

1. Download OT source code for Linux (in Repository)
2. Open terminal
3. CD to OT source code folder
4. Run Command to compile OT: g++ -std=c++11 *.cpp -pthread -lsqlite3 -o OT

Mac and Linux (if you manually built sqlite3 .o file, make sure sqlite3 .o file is in same folder as OT source code):

1. Download OT source code for Mac or Linux (in Repository)
2. Open terminal
3. CD to OT source code folder
4. Run command to compile OT: g++ -std=c++11 *.cpp -pthread sqlite3.o -o OT

Windows (Visual Studio 2017):

1. Download OT source for Windows (in Repository)
2. Open Visual Studio 2017
3. Create a New Project
4. Import the OT source code files
5. Go to Project->Properties and do the following:
   • Set Configuration to "All Configurations"
   • Set Platform to "All Platforms"
   • In Configuration Properties->VC++ Directories add C:\Path\To\sqlite3; to "Include Directories"
   • In Configuration Properties->VC++ Directories add C:\Path\To\sqlite; to "Include Libraries"
   • In C/C++->General add C:\Path\To\sqlite3; to "Additional Include Directories" and "Additional #using Directories"
   • In Linker->General add C:\Path\To\sqlite; to "Additional Library Directories"
   • In Linker->Input add C:\Path\To\sqlite\sqlite3.lib; in "Additonaly Dependencies
   • Make sure when you add these paths that there are ';' seperating all paths/object in the line.
6. For debugging, make sure Debug and x64 are selected before running
   • If debugging, make sure you set the debugging command arguments. See "How to run OT" below.
7. For compiling, make sure Release and x64 are selected before running

How to run OT

• CD to the directory containing the OT executable

  • The command line arguments for OT are as follows: query_file_path endonuclease cspr_file_path db_file_path output_file_path CASPERinfo_file_path max_num_mismatches threshold detailed_output_bool avg_output_bool hsu_matrix_name

• Example command: ./OT query.txt asCas12 myfile_asCas12.cspr myfile_asCas12_repeats.db output.txt CASPERinfo 5 0.05 TRUE FALSE "MATRIX:HSU MATRIX-asCas12-2016"