CRISPRMatchGUI

CRISPRMatch is no longer actively maintained.

We release new CRIPSR data analysis software: CrisprStitch .

Brief introduction

The Graphical User Interface(GUI) for CRISPRMatch--An automatic calculation and visualization tool for high-throughput CRISPR genome-editing data analysis

I. Requirements(软件所需依赖包)

Anaconda
python3
bwa
samtools
FLASH
pyqt5

[Note:] Using Anaconda to Install all packages (bwa,samtools,picard,FLASH) ##应用conda统一安装即可，方便快捷

II. Manually Install（手动安装，非虚拟机）

CentOS Linux release 7.3.1611 (terminal)

1. Install Anaconda
   

$ yum install wget git  ##安装git和wget程序
$ mkdir /home/software  ##创建下载软件的文件夹，这里以software为例
$ cd /home/software     ##进入到software文件夹下
$ wget https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh  ##下载linux对应的conda版本，注意尽量选择3.5版本的！
$ bash Anaconda3-5.0.1-Linux-x86_64.sh  ##用bash命令安装conda

2. Install required packages ##利用conda安装所有依赖包（建议用清华软件源镜像替换，缩短安装时间）

$ conda install bwa \             ##用\符号和回车分隔多个软件
                samtools \  
                pyqt=5.6 \  
                flash \ 
                matplotlib \  
                pysam \  
                pandas \  
                argparse \  
                numpy \

Note: To ensure the tool working, please using Anaconda to install all packages (bwa,samtools,pyqt,FLASH ...)

3. Download CRISPRMatchGUI and test ##下载本软件的软件包

$ cd /home/software   ##进入到software文件夹下
$ git clone https://github.com/zhangtaolab/CRISPRMatchGUI.git  ##利用git方式下载本软件包
$ cd /home/software/CRISPRMatchGUI/   ##进入本软件文件夹
$ python3 /home/software/CRISPRMatchGUI/start.py  ##使用python3打开软件包中的start.py程序，即可实现软件运行
  

III. Start running（运行方法）

1. Video manual(用户手册)
   

(1)CRISPRMatch虚拟机使用教程

• Link: https://v.youku.com/v_show/id_XMzgwODc4ODQ2NA==.html?spm=a2h3j.8428770.3416059.1

(2)双端测序数据合并教程

• Link: https://v.youku.com/v_show/id_XMzkzMTY5NTEwOA==.html?scm=20140719.manual.114461.video_XMzkzMTY5NTEwOA==

(3)拆分混池测序结果(带有barcode信息)

• Link: https://v.youku.com/v_show/id_XMzkzMTY5MzY4NA==.html?scm=20140719.manual.114461.video_XMzkzMTY5MzY4NA==

(4)虚拟机读取usb设备(改方法可实现大数据集计算)

• Link: https://v.youku.com/v_show/id_XMzk0MDgyMjA2MA==.html?scm=20140719.manual.114461.video_XMzk0MDgyMjA2MA==

2. Mirroring file for Windows (虚拟机下载地址)
   

• Link: https://pan.baidu.com/s/1L8KPij9SP2Mp9v7RYgS5_w code: CPF1

3. Files for mutation calculation(编辑计算所需三个信息文件)
   

• File1: Genome-editing target sequences
  Fasta format example
• File2: NGS samples information 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
  note: At present, two repeats are supported
  example:
  group information
• Note: the information files File1, File2 and File3 are required!

4. Merge paired-end reads(运行双端测序数据合并程序)
   

$ cd /home/software/CRISPRMatchGUI/               ##进入本软件文件夹
$ python3 /home/software/CRISPRMatchGUI/merge.py  ##运行双端测序数据合并

• example:
  paired-end reads

5. Split sequencing file(运行拆分混池测序结果)
   

$ cd /home/software/CRISPRMatchGUI/               ##进入本软件文件夹 
$ python3 /home/software/CRISPRMatchGUI/split.py  ##运行拆分混池测序程序