Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
Methods Mol Biol. 2025;2856:71-78. doi: 10.1007/978-1-0716-4136-1_5.
Hi-C reads, which represent ligation events between different regions of the genome, must be processed into matrices of interaction frequencies for downstream analysis. Here, I describe a procedure for mapping Hi-C reads to the genome and conversion of mapped reads into the HOMER tag directory format and interaction matrix format for visualization with Juicebox. The method is demonstrated for the mouse composite X chromosome in which reads from the active and inactive X chromosomes are combined after mock DMSO treatment or targeted degradation of cohesin.
Hi-C 读取代表基因组不同区域之间的连接事件，必须经过处理才能转化为交互频率矩阵，以便下游分析。在这里，我描述了一种将 Hi-C 读取映射到基因组，并将映射读取转换为 HOMER 标签目录格式和交互矩阵格式的方法，以便与 Juicebox 进行可视化。该方法用于模拟二甲亚砜处理或靶向破坏黏连蛋白后，来自活性和失活 X 染色体的读取的复合 X 染色体的小鼠。
