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. 2020 Mar;30(3):447–458. doi: 10.1101/gr.257832.119

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© 2020 Rowley et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 1. — Overview of SIP. (A) The graphical user interface provides options to specify a Juicer-derived .hic file or processed data, the output directory, and chromosome size file. It also allows adjustment of the various parameters shown. (B) SIP uses image-based detection to create a long list of candidate loops, which is further filtered based on properties of the distance-normalized matrix.