Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg 79110, Germany.
Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Bioinformatics. 2021 Aug 4;37(14):2053-2054. doi: 10.1093/bioinformatics/btaa924.
Single-cell Hi-C research currently lacks an efficient, easy to use and shareable data storage format. Recent studies have used a variety of sub-optimal solutions: publishing raw data only, text-based interaction matrices, or reusing established Hi-C storage formats for single interaction matrices. These approaches are storage and pre-processing intensive, require long labour time and are often error-prone.
The single-cell cooler file format (scool) provides an efficient, user-friendly and storage-saving approach for single-cell Hi-C data. It is a flavour of the established cooler format and guarantees stable API support.
The single-cell cooler format is part of the cooler file format as of API version 0.8.9. It is available via pip, conda and github: https://github.com/mirnylab/cooler.
Supplementary data are available at Bioinformatics online.
单细胞 Hi-C 研究目前缺乏一种高效、易用且可共享的数据存储格式。最近的研究使用了各种不太理想的解决方案：仅发布原始数据、基于文本的交互矩阵，或重新使用现有的 Hi-C 存储格式来存储单个交互矩阵。这些方法在存储和预处理方面很密集，需要很长的时间，并且常常容易出错。
单细胞 cooler 文件格式 (scool) 为单细胞 Hi-C 数据提供了一种高效、用户友好且节省存储空间的方法。它是已建立的 cooler 格式的一个变体，并保证了稳定的 API 支持。
单细胞 cooler 格式是自 API 版本 0.8.9 起 cooler 文件格式的一部分。它可以通过 pip、conda 和 github（https://github.com/mirnylab/cooler）获得。
补充数据可在《Bioinformatics》在线获取。
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