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. 2020 Sep 30;21:256. doi: 10.1186/s13059-020-02167-0

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — A comparison between Mustache, SIP, and HiCCUPS reported loop calls in a region of chromosome 1 for the GM12878 cell line (50.75–51.75 Mb). The Hi-C contact map is rotated 45^∘ such that the main diagonal is horizontal (top). Below the contact map, we report genomic coordinates, gene annotations (genes on the negative strand are shown in red color), CTCF motifs and their orientation, and ChIP-seq signals for SMC3, CTCF, RAD21, H3K4me3, and H3K27ac (coverage tracks plotted by HiGlass). The bottom row demonstrates loop calls as arcs connecting two loci labeled by the initial letter of the methods by which they are detected (“M” for Mustache, “S” for SIP, and “H” for HiCCUPS)