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Fig. 3 | BMC Bioinformatics

Fig. 3

From: HiCcompare: an R-package for joint normalization and comparison of HI-C datasets

Fig. 3

MD plot data visualization and the effects of different normalization techniques. MD plots of the differences M between two replicated Hi-C datasets (GM12878 cell line, chromosome 11, 1 MB resolution, DpnII and MboI restriction enzymes) plotted vs. distance D between interacting regions. a Before normalization, b after loess joint normalization, c ChromoR, d Iterative Correction and Eigenvector decomposition (ICE), e Knight-Ruiz (KR), f Sequential Component Normalization (SCN). The general shift of the data above M = 0 is due to one of the Hi-C libraries having more total reads. The trends emphasized by the loess curve imposed on the data are due to distance dependent between-dataset biases which only HiCcompare’s joint normalization procedure can successfully remove

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