Useful commands for 4DGB project
================================

Generating a ``.hic`` file.
---------------------------

Below is an example of using `juicer tools <https://github.com/aidenlab/juicer/wiki/>`_ for Hi-C data preprocessing.
The example commands below assume the user has generated an output data file from the juicer pipeline as an ``in.short`` file.
The example below demonstrates how to generate data for a single chromosome (chromosome 22) with ``KR`` corrected hi-c contact counts.

.. code-block::

    ## change directory and make alias callable in this instance
    cd ./hic-converter
    shopt -s expand_aliases

    ## Set the juicer alias
    alias juicer='java -Xms512m -Xmx2048m -jar ./tools/juicer_tools_1.22.01.jar'

    ## Splitting off single chromosome (chromosome 22) data from large Hi-C file that is KR balanced and resolved at 200 kb
    juicer pre in.short out.chr22.200kb.hic ./sizes/chr22.size.bed -r 200000 -k KR 
    
Formatting with Juicer Pre
--------------------------

Using ``juicer pre`` to extract contacts along chromosome 1, with 200 kb resolution, and Knight Runiz correction.

.. code-block::

    juicer pre -k KR -r 200000 merged_nodups.txt.gz output.chr1.hic chr1.size.bed``

Example data within ``chr1.size.bed`` file used above.

.. code-block::

    chr1	248956422