National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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.
Genes (Basel). 2020 Mar 10;11(3):289. doi: 10.3390/genes11030289.
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.
了解长距离基因组距离上靶基因调控元件的作用机制变得越来越重要。3C（染色体构象捕获）及其衍生方法现在广泛应用于研究三维（3D）基因组结构和基因调控。仅消化-连接 Hi-C（DLO Hi-C）是一种新的高效、经济的全基因组染色体构象捕获技术。在这里，我们介绍了 DLO Hi-C 工具，这是一个灵活多样的流水线，用于从原始测序reads 处理 DLO Hi-C 数据到归一化接触图谱，并为不同步骤提供质量控制。它包括更有效的迭代映射和链接器过滤。我们将 DLO Hi-C 工具应用于不同的 DLO Hi-C 数据集，并证明了它在多线程处理大数据方面的能力。DLO Hi-C 工具适用于处理 DLO Hi-C 和原位 DLO Hi-C 数据集。它方便高效，适用于 DLO Hi-C 数据处理。
