ChIA-PET V3 Tool: ChIA-PET, HiChIP and PLAC-Seq data analysis tool

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a technology to study genome-wide long-range chromatin interactions bound by protein factors. ChIA-PET Tool V3, a software package for automatic processing of ChIA-PET sequence data, including:

1. linker filtering for ChIA-PET and BL-HiChIP data

2. mapping the paired-end reads to a reference genome

3. purifying the mapped reads

4. dividing the reads into different categories

5. peak calling

6. interaction/loop calling

7. visualizing the results

Installation

• Please download and install the tools (see Installation)

The functions you can use CPT3 to do:

• Linker filter: linker filtering for ChIA-PET and BL-HiChIP data

• Alignment: Align paired-end reads

• PET divide: dividing the reads into different categories

• Peak calling: peak calling with MACS2

• Loop calling: interaction/loop calling

• Loop calling: visualizing the results and report a html

Contents

Basic Use

• Installation
• Example Data
• Build index
• Pipeline
• Linker filter
• Alignment
• PET divide
• Peak calling
• Loop calling

function/visulization

While developing CPT3, we continuously strive to create software that fulfills the following criteria:

• raw fastq/fastq.gz reads quality control with or without linker filter and efficiently alignment

• dividing the PETs into different categories for ChIA-PET or HiChIP data.

• calling peaks with MACS2 or SPP methods.

• efficiently calling loops

• generation of highly customizable visulization

Citation

Please cite CPT3 as follows:

cite Li G, Sun T, Chang H, Cai L, Hong P, Zhou Q. Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3). Genes (Basel). 2019 Jul 22;10(7):554. doi: 10.3390/genes10070554. PMID: 31336684; PMCID: PMC6678675 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678675/

Tip

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