HiCRes：一种用于估计和预测 Hi-C 文库基因组分辨率的计算方法。
HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries.
机构信息
Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA.
In silichrom Ltd, First Floor, Angel Court, 81 St Clements St, Oxford OX4 1AW, UK.
出版信息
Nucleic Acids Res. 2022 Apr 8;50(6):e35. doi: 10.1093/nar/gkab1235.
Abstract
Three-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. Hi-C is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a library is an essential step in any Hi-C experimental design. Here, we present the mathematical concepts to estimate the resolution of a dataset and predict whether deeper sequencing would enhance the resolution. We have developed HiCRes, a docker pipeline, by applying these concepts to several Hi-C libraries.
摘要
染色质的三维（3D）构象对于以细胞类型特异性的方式严格调控基因表达模式和 DNA 复制至关重要。Hi-C 是一种测量全基因组 3D 染色质相互作用的关键技术。估计和预测文库的分辨率是任何 Hi-C 实验设计的重要步骤。在这里，我们提出了用于估计数据集分辨率并预测更深测序是否会提高分辨率的数学概念。我们通过将这些概念应用于几个 Hi-C 文库，开发了 HiCRes，这是一个 Docker 管道。
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