Useful commands for 4DGB project

Generating a .hic file.

Below is an example of using juicer tools 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.

## 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.

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