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

  • Author(s): Roayaei Ardakany, Abbas;
  • Gezer, Halil Tuvan;
  • Lonardi, Stefano;
  • Ay, Ferhat
  • et al.
Abstract

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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