HiCmapTools: a tool to access HiC contact maps

Jia-Ming Chang,Wei-Ting Chang,Giacomo Cavalli,Yi-Fu Weng,Fu-An Lin

doi:10.1186/s12859-022-04589-y

Abstract

BackgroundWith the development of HiC technology, more and more HiC sequencing data have been produced. Although there are dozens of packages that can turn sequencing data into contact maps, there is no appropriate tool to query contact maps in order to extract biological information from HiC datasets.ResultsWe present HiCmapTools, a tool for biologists to efficiently calculate and analyze HiC maps. The complete program provides multi-query modes and analysis tools. We have validated its utility on two real biological questions: TAD loop and TAD intra-density.ConclusionsHiCmapTools supports seven access options so that biologists can quantify contact frequency of the interest sites. The tool has been implemented in C++ and R and is freely available at https://github.com/changlabtw/hicmaptools and documented at https://hicmaptools.readthedocs.io/.

Highlights

With the development of HiC technology, more and more HiC sequenc‐ ing data have been produced
HiC data has shown chromosome structure to be formed by 3D folding of a higher-order unit, the topologically associating domain (TAD) [14,15,16]
In Drosophila, TADs can be further classified into four epiTADs—active, null, PcG, and HP1—based on ChIP-seq binding profiles [14]

Summary

Introduction

With the development of HiC technology, more and more HiC sequenc‐ ing data have been produced. There is no suitable tool to access HiC map results except for visualization (Table 1), that is, no systematic way to extract HiC contact information for a specific query. We have developed HiCmapTools, which helps biologists efficiently query HiC maps and perform permutation tests. It supports seven query modes and attempts to cover the most frequent needs of biologists who use HiC to study chromatin contacts and their putative function.

Results

Conclusion