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

.. image:: media/BatMeth2-pipeline.jpg

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 :doc:`function/install`)

The functions you can use CPT3 to do:

* :doc:`function/Linkerfilter`: linker filtering for ChIA-PET and BL-HiChIP data
* :doc:`function/Alignment`: Align paired-end reads
* :doc:`function/PETdivide`: dividing the reads into different categories
* :doc:`function/peakcall`: peak calling with MACS2
* :doc:`function/loopcall`: interaction/loop calling 
* :doc:`function/loopcall`: visualizing the results and report a html 


Contents
^^^^^^^^

.. toctree::
   :caption: Basic Use
   :maxdepth: 1

   function/install
   function/example
   function/bdindex
   function/Pipeline
   function/Linkerfilter
   function/Alignment
   function/PETdivide
   function/peakcall
   function/loopcall

  
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 <https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3>`__.