hic-converter

A collection of tools, commands, and data used in preprocessing and setup of Hi-C data for the 4D-Genome Browser (4DGB) Project.

Example usage

Converting contact matrix from HiCExplorer as an .h5 file to a contact matrix with .hic

## Activate hic-explorer environment
conda activate hicexplorerenv

## Change directory to tools
cd ./hic-converter/tools

## Convert the .h5 file to .hic formated file for Mus musculus chromosome 13
./h5.to.hic.sh -m ../data/h5/SRR1956527_chr13.h5 -g ../data/sizes/mm10.chr13.size.bed -o ../data/hic/SRR1956527_chr13.200kb.hic

Generating a .hic file from .summary.txt.gz file

## 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.mus.chr13.summary.txt.gz -g mm9 -c chr13 -O ../data/hic/GSM2667262_WT1.HiC.rep1.mus.chr13.200kb.hic

Convert juicer merged_nodups (long format) file for chromosome 22 to .hic

## Activate hic-explorer environment
conda activate hicexplorerenv

## Change directory to tools
cd ./hic-converter/tools

## Envoke our long to chrom hic function
./long.to.chrom.hic.py -i ../data/long/merged_nodups.chr22.subsampled.txt.gz -g ../data/sizes/GRCh38.chr22.size.bed -c chr22 -O ../data/hic/chr22.10kb.hic -R 10000

Installation

Download and set up

## Clone this repo
git clone git@github.com:4DGB/hic-converter.git

## Make scripts within the *tools* directory executable
chmod +x ./hic-converter/tools/*.sh ./hic-converter/tools/*.py

Generate a conda environment with an installation of HiCExplorer

conda create -n hicexplorerenv hicexplorer -c bioconda -c conda-forge

Other needed python libraries

os, argparse, numpy, pandas, gzip, subprocess

Dependencies

Juicer

Juicer tools jar file

Scripts here were developed using version 1.22.01 (also stored here on this repo).

Python

Anaconda

A conda environment is generated to install HiCExplorer

Useful commands for 4DGB project

Example using juicer tools for Hi-C data preprocessing

## 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

Example Hi-C creation and formatting

Pipeline(s) outline and file outputs

R1.fastq.gz, R2.fastq.gz -> HiCExplorer -> output.h5 -> (.h5 to .hic, see above)

or

R1.fastq.gz, R2.fastq.gz -> juicer pipeline -> merged_nodups.txt.gz -> juicer tools (see below)

Formatting with Juicer Pre

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

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

chr1	248956422

Work Cited

• Marks et al. "Dynamics of gene silencing during X inactivation using allele-specific RNA-seq." Genome biology 16.1 (2015): 1-20.

• Durand et al. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments." Cell systems 3.1 (2016): 95-98.

• Wang et al. "SMCHD1 merges chromosome compartments and assists formation of super-structures on the inactive X." Cell 174.2 (2018): 406-421.

• Wolff et al. "Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization." Nucleic acids research 48.W1 (2020): W177-W184.

• Lappala et al. "Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome." Proceedings of the National Academy of Sciences 118.42 (2021): e2107092118.