The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.

ABSTRACT: The 3D chromatin structure modeling by chromatin interactions derived from Hi-C experiments is significantly challenged by the intrinsic sequencing biases in these experiments. Conventional modeling methods only focus on the bias among different chromatin regions within the same experiment but neglect the bias arising from different experimental sequencing depth. We now show that the regional interaction bias is tightly coupled with the sequencing depth, and we further identify a chromatin structure parameter as the inherent characteristics of Hi-C derived data for chromatin regions. Then we present an approach for chromatin structure prediction capable of relaxing both kinds of sequencing biases by using this identified parameter. This method is validated by intra and inter cell-line comp

SUBMITTER: Peng C 

PROVIDER: S-EPMC3799458 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature