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. 2022 Dec 2;13:7426. doi: 10.1038/s41467-022-35231-3

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© The Author(s) 2022

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a TAD boundary pileups for left boundaries predicted by RefHiC. b Number of predicted left TAD boundaries supported by ChIP-seq identified CTCF binding sites (positive strand only), for RefHiC, RobusTAD, and Insulation score. c–i Benchmarking RefHiC against 13 other TAD callers on TAD annotation. c Number of TADs predicted by different tools, and proportion of predicted TAD boundary pairs that are supported by CTCF ChIA-PET data. Size (d), and mean interaction frequency (observed/expected) (e) of TAD predictions. The number of TADs used to generated box plots are provided in (c). In each box, the upper edge, central line, and lower edge represent the 75th, 50th, and 25th percentile, respectively. Upper whiskers represent 75th percentile + 1.5 × interquartile range (IQR), lower whiskers represent minimum values, and dots represent samples above the 75th percentile + 1.5 × IQR. f Enrichment of CTCF, RAD21, and SMC3 peak signals at TAD boundaries. g Fraction of TADs predicted by each caller with a significant (high or low) H3K27me3/H3K36me3 log10-ratio (FDR < 0.1). Jaccard index of predicted TAD boundaries (h) and Concordance between TADs (i) predicted on high-coverage GM12878 data (2B valid read pairs) compared to those predicted on downsampled Hi-C data. Note: a–g are based on a downsampled GM12878 Hi-C data set that containing 500M valid read pairs).