Build index
===========

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

.. contents:: 
    :local:

Genome index
------------

* Have a fasta-formatted reference file ready, and then make the neccessary pairing data-structure based on FM-index.


.. code:: bash

    bwa index genome.fa


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