Peak calling
============

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

.. contents:: 
    :local:

peak calling
------------

CPT3 contains peak calling method with MACS2 (suggest) or SPP method.

.. code:: bash

    $ java -jar ChIA-PET.jar --macs2 macs2 \
    macs2 path, using macs2 callpeak to detect anchor peak with alignment file. default: N



.. tip:: For feature requests or bug reports please open an issue `on github <https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3>`__.