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SnapHiC: a computational pipeline to map chromatin contacts from single cell Hi-C data

By Miao Yu, Armen Abnousi, Yanxiao Zhang, Guoqiang Li, Lindsay Lee, Ziyin Chen, Rongxin Fang, Jia Wen, Quan Sun, Yun Li, Bing Ren, Ming Hu

Posted 15 Dec 2020
bioRxiv DOI: 10.1101/2020.12.13.422543

Single cell Hi-C (scHi-C) analysis has been increasingly used to map the chromatin architecture in diverse tissue contexts, but computational tools to define chromatin contacts at high resolution from scHi-C data are still lacking. Here, we describe SnapHiC, a method that can identify chromatin loops at high resolution and accuracy from scHi-C data. We benchmark SnapHiC against HiCCUPS, a common tool for mapping chromatin contacts in bulk Hi-C data, using scHi-C data from 742 mouse embryonic stem cells. We further demonstrate its utility by analyzing single-nucleus methyl-3C-seq data from 2,869 human prefrontal cortical cells. We uncover cell-type-specific chromatin loops and predict putative target genes for non-coding sequence variants associated with neuropsychiatric disorders. Our results suggest that SnapHiC could facilitate the analysis of cell-type-specific chromatin architecture and gene regulatory programs in complex tissues.

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