Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Open2C, Open Chromosome Collective, Cambridge, MA, USA.
Methods Mol Biol. 2025;2856:241-262. doi: 10.1007/978-1-0716-4136-1_14.
Single-cell Hi-C (scHi-C) is a collection of protocols for studying genomic interactions within individual cells. Although data analysis for scHi-C resembles data analysis for bulk Hi-C, the unique challenges of scHi-C, such as high noise and protocol-specific biases, require specialized data processing strategies. In this tutorial chapter, we focus on using pairtools, a suite of tools optimized for scHi-C data, demonstrating its application on a Drosophila snHi-C dataset. While centered on pairtools for snHi-C data, the principles outlined are applicable across scHi-C variants with minor adjustments. This educational chapter aims to guide researchers in using open-source tools for scHi-C analysis, emphasizing critical steps of contact pair extraction, detection of ligation junctions, filtration, and deduplication.
单细胞 Hi-C（scHi-C）是一系列用于研究单个细胞内基因组相互作用的方案。尽管 scHi-C 的数据分析类似于 bulk Hi-C 的数据分析，但 scHi-C 的独特挑战，如高噪声和特定于方案的偏差，需要专门的数据处理策略。在本教程章节中，我们专注于使用 pairtools，这是一套针对 scHi-C 数据优化的工具，并展示了它在果蝇 snHi-C 数据集上的应用。虽然以 snHi-C 数据的 pairtools 为中心，但概述的原则适用于少数调整后的 scHi-C 变体。本教育性章节旨在指导研究人员使用开源工具进行 scHi-C 分析，强调了接触对提取、连接点检测、过滤和去重等关键步骤。
