期刊
GENOME BIOLOGY
卷 21, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s13059-020-02167-0
关键词
Contact maps; Genome architecture; Chromatin loops; Hi-C; Micro-C; HiChIP; ChIA-PET; Promoter-enhancer interactions; CTCF; Cohesin
资金
- NIH [R35-GM128938]
- NSF [IIS-1814359]
We present MUSTACHE, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. MUSTACHE employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps. MUSTACHE is scalable to kilobase-resolution maps and reports loops that are highly consistent between replicates and between Hi-C and Micro-C datasets. Compared to other loop callers, such as HiCCUPS and SIP, MUSTACHE recovers a higher number of published ChIA-PET and HiChIP loops as well as loops linking promoters to regulatory elements. Overall, MUSTACHE enables an efficient and comprehensive analysis of chromatin loops. Available at: https://github.com/ay-lab/mustache.
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