phytoCRISP-Ex
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phytoCRISP-Ex is a rational and flexible tool for finding Cas9 target sites with low/no off-targeting potential.


System Requirements
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1. OS Platform:- Linux
2. Perl 4.0, or above


Required Input Files
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1. Input file in fasta format. (.fasta)
2. Genome file in fasta format. (.fasta)


Inputs Example Files
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1. INPUT:	/phytoCRISP-Ex_v1.0/EXAMPLE/ExampleQuery.fasta
2. Genome:	/phytoCRISP-Ex_v1.0/EXAMPLE/ExampleGenome.fasta


Output Files													
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1. QuerySequenceHeader.csv


Installation
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1. Download phytoCRISP-Ex_v1.0.tar.gz
2. gunzip phytoCRISP-Ex_v1.0.tar.gz
3. tar -vxf phytoCRISP-Ex_v1.0.tar
4. cd phytoCRISP-Ex_v1.0/
5. ./install.sh	<phytoCRISPex_INTALLATION_PATH>		-------  configures the installtion path and install the program
6. source phytoCRISPex_INSTALLATION_PATH/crispex_profile	[NOTE:Please run this command prior to the execution of phytoCRISP-Ex]
7. Using same terminal move to the directory containing the input files and run phytoCRISP-Ex [phytoCRISPex_INSTALLATION_PATH/phytoCRISPex -in <Query.fasta> -db <Genome.fasta> <NGG/NAG> <G/N>]


Usage
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1. Using terminal, move to the working directory containing your input files (Query and Genome Fasta files).
2. run phytoCRISP-Ex. using command "phytoCRISPex_INSTALLATION_PATH/phytoCRISPex -in [Query.fasta] -db [Genome.fasta] [PAM sequence] [CRISPR target Start]"		Example run: phytoCRISPex_INSTALLATION_PATH/phytoCRISPex -in ExampleQuery.fasta -db ExampleGenome.fasta NGG G


DeveloperZ Information
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Achal Rastogi
PhD, ENS

NOTES:
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1. Being in the directory containing input files is a prerequisite for running phytoCRISP-Ex, to avoid output errors.
2. Take care of the inputs, wrong inputs may fetch you with wrong results.
3. Script mounted and tested on Ubuntu x86_64