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.
CITATION STYLE
Roayaei Ardakany, A., Gezer, H. T., Lonardi, S., & Ay, F. (2020). Mustache: Multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation. Genome Biology, 21(1). https://doi.org/10.1186/s13059-020-02167-0
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