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. 2022 Feb 10;23(1):64.
doi: 10.1186/s12859-022-04589-y.

HiCmapTools: a tool to access HiC contact maps

Jia-Ming Chang  1 , Yi-Fu Weng  2 , Wei-Ting Chang  2 , Fu-An Lin  2 , Giacomo Cavalli  3
Affiliations

HiCmapTools: a tool to access HiC contact maps

Jia-Ming Chang et al. BMC Bioinformatics. .

Abstract

Background: With 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.

Results: We 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.

Conclusions: HiCmapTools 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/ .

Keywords: 3D genome; Hi-C; Juicer; Topologically Associating Domains (TADs); hicpipe.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Illustration of query modes. Numbers indicate the corresponding query modes. HiC data is Drosophila chr3R:2000k..10000k [14]
Fig. 2
Fig. 2
Plot of the permutation test. Density shows the frequency of the permutation test. Query frequency is highlighted as a red vertical line
Fig. 3
Fig. 3
Boxplot of loop frequency regarding epiTADs
Fig. 4
Fig. 4
Boxplot of average intra-TAD contact frequencies regarding epiTADs
See this image and copyright information in PMC

References

    1. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002;295:1306–1311. doi: 10.1126/science.1067799. - DOI - PubMed
    1. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) Nat Genet. 2006;38:1348–1354. doi: 10.1038/ng1896. - DOI - PubMed
    1. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16:1299–1309. doi: 10.1101/gr.5571506. - DOI - PMC - PubMed
    1. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–293. doi: 10.1126/science.1181369. - DOI - PMC - PubMed
    1. Forcato M, Nicoletti C, Pal K, Livi CM, Ferrari F, Bicciato S. Comparison of computational methods for Hi-C data analysis. Nat Methods. 2017;14:679–685. doi: 10.1038/nmeth.4325. - DOI - PMC - PubMed

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