hicmaptools

It is a commend line tool to access HiC maps. The complete program provides multi-query modes and analysis tools. A detailed document is avaiable in the readthedocs of HiCmapTools.

Prerequisites

hicmaptools compilation requires the following tools installed on your system make, gcc-c++ and R.

Compile/Installation

Clone the git repository on your computer with the following command:

git clone git@github.com:cbcrg/hicmaptools.git hicmaptools

Make sure you have installed the required dependencies listed above. When done, move in the project root folder named hicmaptools and enter the following commands:

$ cd src
$ make

The binary will be automatically copied to the path hicmaptools/bin.

$ make install

The binary will be automatically copied to the path specified by the environment variable $USER_BIN (check that it exists before run the make command).

Quick start

hicmaptools -in_map in.binmap -in_bin in.bins QUERY_MODE query.bed -output out_file.tsv
or
hicmaptools -in_hic in.hic [-in_hic_norm NONE] [-in_hic_resol 10000] QUERY_MODE query.bed -output out_file.tsv

input:  
        -in_map        text .n_contact or binary .binmap by genBinMap commend 
        -in_bin        the bin file for contact map, .bins
        or
        -in_hic        .hic file generated by Juicer
        -in_hic_norm   optional, a normalization method (NONE|VC|VC_SQRT|KR, default: NONE)
        -in_hic_resol  optional, a resolution used to bin .hic (default: 10000)
        or
        -in_gin        .gin file in ginteractions format
    
QUERY_MODE: 
        -bait         calculate average contacts from downstream to upstream of interested position
    
        -local       list all contacts inside an interval

        -loop        contact intensity between two ends of a loop
        
        -pair        contacts between a pair region
        
        -sites       contacts between sites

        -submap      sub contact map of interested regions

        -TAD         sum and average of contacts inside TAD region
    
other parameters:
        -ner_bin     check neighbouring bins for bait mode, (default: 10)
        -random      the size of the shffule sample (default: 100)

For instance:

hicmaptools -in_map examples/fly_30k.binmap -in_bin examples/fly_30k.bins -bait examples/bait.bed -output temp.tsv

References

• Jia-Ming Chang, Yi-Fu Weng, Wei-Ting Chang, Fu-An Lin, Giacomo Cavalli. HiCmapTools: A tool to access HiC contact maps. BMC Bioinformatics 23, 64 (2022).
• The parser of .hic is adapted from straw.
  • Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. "Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom." Cell Systems 3(1), 2016.