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Open AccessArticle

The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis

by Ping Hong 1,2,†, Hao Jiang 1,2,†, Weize Xu 3,4,5,†, Da Lin 3,4,5,†, Qian Xu 1,2, Gang Cao 3,4,5,* and Guoliang Li 1,2,*
1
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
2
Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
3
State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
4
College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
5
College of Bio-Medical and Health, Huazhong Agricultural University, Wuhan 430070, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2020, 11(3), 289; https://doi.org/10.3390/genes11030289
Received: 27 January 2020 / Revised: 25 February 2020 / Accepted: 7 March 2020 / Published: 10 March 2020
(This article belongs to the Section Technologies and Resources for Genetics)
It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing. View Full-Text
Keywords: 3D genomics; DLO Hi-C; linker detection; iteration mapping 3D genomics; DLO Hi-C; linker detection; iteration mapping
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Hong, P.; Jiang, H.; Xu, W.; Lin, D.; Xu, Q.; Cao, G.; Li, G. The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis. Genes 2020, 11, 289.

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