Welcome to the instruction page for using this tool offline. You can simply download all the program files in your system and run the code in linux operationg
system (preferably Ubuntu). Be sure that the: 

1. python(version not less than 3) is installed in your system.
2. Bowtie is installed and you know the location of it (lets say /usr/bin/ in our case).

Simply, Navigate in the terminal to the location where all the required files are stored and run the following command.


python3  ge.py --input elegans.fa   --index elegans/WBcel235 --output out --bowtie /usr/bin/

ge.py is the main program code to run the off-target analysis
--input is used to mention the input file in fasta format.
--index is the folder named elegans contains the index files of genome elegans (or you may prepare using bowtie) with name WBce1235
--output is used with out as the name of the folder in which the output files will be automatically stored after you run the code successfully.
The code automatically takes NGG as default PAM or can otherwise be specified using --pam and max mismatch 4

ge.py [-h] --input <file> --index <file> [--bowtie <folder>] [--targetSize <int>]
             [--pam {NGG,NRG,TTTN,NNGRRT,NNNNGATT,NNAGAAW,NAAAAC}] [--totalMM <int>] 
              [--output <folder>]
