Installation

CPT3: An Integrated Package for ChIA-PET, HiChIP and PLAC-Seq data analysis.

Requirements

• JDK>=1.8(https://www.oracle.com/technetwork/java/javase/downloads/index.html)

• BWA(http://bio-bwa.sourceforge.net/)

• SAMtools(http://samtools.sourceforge.net/)

• BEDTools(https://bedtools.readthedocs.io/en/latest/)

• R(https://www.r-project.org/)

• R package grid(install.packages("grid"))

• R package xtable(install.packages("xtable"))

• R package RCircos(install.packages("RCircos"))

• fastp, raw reads as input need.

Install

a) git clone git@github.com:GuoliangLi-HZAU/ChIA-PET_Tool_V3.git
b) Change directory into the top directory of ChIA-PET_Tool_V3
    $ cd ChIA-PET_Tool_V3
c) Type
    $ java -jar ChIA-PET.jar --help

Tip

For feature requests or bug reports please open an issue on github.