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

ABSTRACT:

Motivation

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 separated by 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.

Results

We present Serpentine, a fast, flexible procedure operating on raw data, which cons

SUBMITTER: Baudry L 

PROVIDER: S-EPMC7320618 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature