Activate and inactive X
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:
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
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.
## 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