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Serpentine: a flexible 2D binning method for differential Hi-C analysis

Abstract : Hi-C contact maps reflect the relative contact frequencies between pairs of genomic loci, quantified through deep sequencing. Differential analyses of these maps enable downstream biological interpretations. However, the multi-fractal nature of the chromatin polymer inside the cellular envelope results in contact frequency values spanning several orders of magnitude: contacts between loci pairs at large genomic distances are much sparser than closer pairs. The same is true for poorly-covered regions such as repeated sequences. Both distant and poorly covered regions translate into low signal-to-noise ratios. There is no clear consensus to address this limitation.
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Lyam Baudry, Gaël Millot, Agnès Thierry, Romain Koszul, Vittore Scolari. Serpentine: a flexible 2D binning method for differential Hi-C analysis. Bioinformatics, Oxford University Press (OUP), 2020, ⟨10.1093/bioinformatics/btaa249⟩. ⟨pasteur-02612482⟩

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