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readme.md

CRISPRMatch

Brief introduction

An automatic calculation and visualization tool for high-throughput CRISPR genome-editing data analysis

I. Requirements

Anaconda
python3
bwa
samtools
picard
FLASH

#f03c15 Note: Using Anaconda to Install all packages (bwa,samtools,picard,FLASH)

II. Manually Install

CentOS Linux release 7.3.1611 (terminal)

  1. Install Anaconda
$ yum install wget git
$ mkdir /home/software
$ cd /home/software
$ wget https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh
$ bash Anaconda3-5.0.1-Linux-x86_64.sh
  1. Install required packages
$ conda install bwa \  
                samtools \  
                picard \  
                flash \ 
                matplotlib \  
                pysam \  
                pandas \  
                argparse \  
                numpy \
  • #f03c15 Note: To ensure the tool working, please using Anaconda to install all packages (bwa,samtools,picard,FLASH ...)
  1. Download CRISPRMatch and test
$ cd /home/software
$ git clone https://github.com/zhangtaolab/CRISPRMatch.git
$ python3 /home/software/CRISPRMatch/CRISPRMatch.py -h
  
  usage: CRISPRMatch [-h] [--version] [-b BWA] [-sm SAMTOOLS] [-pi PICARD] -g
                    GENOME -i INPUT -gi GROUPINFO [-s SAVED] [-r RESULT]
                    [-t THREADS] [--docker DOCKER]

  CRISPRMatch is for location finding

  optional arguments:
    -h, --help            show this help message and exit
    --version             show program's version number and exit
    -b BWA, --bwa BWA     bwa path
    -sm SAMTOOLS, --samtools SAMTOOLS
                          samtools path
    -pi PICARD, --picard PICARD
                          picard path
    -g GENOME, --genome GENOME
                          fasta format genome file
    -i INPUT, --input INPUT
                          sample information input file
    -gi GROUPINFO, --groupinfo GROUPINFO
                          group information input file
    -s SAVED, --save SAVED
                          tmp saved folder
    -r RESULT, --result RESULT
                          result saved folder
    -t THREADS, --threads THREADS
                          threads number or how may cpu you wanna use

III. Start running

  1. Files for mutation calculation
  • File1: Genome-editing target sequences
    Fasta format example
  • File2: NGS samples information
    #f03c15 note:
    For CRISPR-Cas9 system, the 'Note' must contain 'gRNA' label.
    For CRISPR-Cpf1 system, the 'Note' must contain 'crRNA' label.
    example:
    sample information
  • File3: NGS group information
    #f03c15 note: At present, two repeats are supported
    example:
    group information
  • Note: the information files File1, File2 and File3 are required!

2. command line example:

(1) For single long reads

$ cd /home/software/CRISPRMatch/
$ python3 CRISPRMatch.py -g sampledata/Samples_gene.fa -i sampledata/sample_infor.txt -gi sampledata/group_info.txt -t 2
- Note: absolute path is preferred when using customer data

(2) For paired-end reads

$ cd /home/software/CRISPRMatch/
$ python3 CRISPRMatch_paired.py -g sampledata2/Samples_gene.fa -i sampledata2/sample_infor.txt -gi sampledata2/group_info.txt -t 2
- Note: absolute path is preferred when using customer data

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