Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation

Genome Biology

Halil Tuvan Gezer¹  Abbas Roayaei Ardakany²  Ferhat Ay³  Stefano Lonardi⁴ 

[1] Centers for Autoimmunity and Cancer Immunotherapy, La Jolla Institute for Immunology, 92037, La Jolla, CA, USA;Computer Science and Engineering, Sabanci University, 34956, Tuzla, Istanbul, Turkey;Centers for Autoimmunity and Cancer Immunotherapy, La Jolla Institute for Immunology, 92037, La Jolla, CA, USA;Computer Science and Engineering, University of California, Riverside, 92521, Riverside, CA, USA;Centers for Autoimmunity and Cancer Immunotherapy, La Jolla Institute for Immunology, 92037, La Jolla, CA, USA;School of Medicine, University of California, San Diego, 92093, San Diego, CA, USA;Computer Science and Engineering, University of California, Riverside, 92521, Riverside, CA, USA;

关键词: Contact maps;    Genome architecture;    Chromatin loops;    Hi-C;    Micro-C;    HiChIP;    ChIA-PET;    Promoter-enhancer interactions;    CTCF;    Cohesin;   

DOI  :  10.1186/s13059-020-02167-0

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY