Activate and inactive X
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Data generated by `Wang `_ *et al.* 2019 and featured in `Lappala `_ *et al.* 2021 were downloaded from the `Gene Expression Omnibus `_ in the ``.summary.txt.gz`` file format.
The first wild-type replicate from the record `GSE99991 `_, with accession record `GSM2667262 `_, was used in analysis and development of the ``summary.to.chrom.hic.py`` executable script ( `listed here `_).
As shown below, this script converts hi-c data in ``.summary.txt.gz`` format to ``.hic``.
The two haplotype resolved ``.summary.txt.gz`` files for chromosome 13, of the first replicate from Wang *et al.* for the wild-type, *cas* and *mus* haplotypes are named (and stored) as follows:
* `GSM2667262_WT1.HiC.rep1.cas.chr13.summary.txt.gz `_
* `GSM2667262_WT1.HiC.rep1.mus.chr13.summary.txt.gz `_
The *cas* and *mus* haplotype names correspond to the activate (Xa) and inactive (Xi) chromosome X states, respectively. The mm9, Mus musculus reference genome was used in analysis.
Generating a ``.hic`` file from a ``.summary.txt.gz``
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Shown below is an example call to the ``summary.to.chrom.hic.py`` command, generating a ``.hic`` file for the *cas*, activate chromosome X haplotype.
These examples may be repeated similarly for generating ``.hic`` data for the *mus* haplotype.
This script (and data) is stored on the associated, `hic-converter `_ git-repository.
.. code-block::
## Change directory to tools
cd ./hic-converter/tools
## Convert a summary.txt.gz file to an .hic file for a single chromosome
./summary.to.chrom.hic.py -i ../data/summary/GSM2667262_WT1.HiC.rep1.cas.chr13.summary.txt.gz -g mm9 -c chr13 -O ../data/hic/GSM2667262_WT1.HiC.rep1.cas.chr13.hic