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

Lyam Baudry (1, 2) , Gaël A Millot (3) , Agnès Thierry (1) , Romain Koszul (1) , Vittore F Scolari (1)

1 Régulation spatiale des Génomes - Spatial Regulation of Genomes
2 SU - Sorbonne Université
3 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB

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.

Domains: Life Sciences [q-bio]; Life Sciences [q-bio]; Quantitative Methods [q-bio.QM]

Lyam Baudry, Gaël A Millot, Agnès Thierry, Romain Koszul, Vittore F Scolari. Serpentine: a flexible 2D binning method for differential Hi-C analysis. Bioinformatics, 2020, ⟨10.1093/bioinformatics/btaa249⟩. ⟨pasteur-02612482⟩