Work

FreeHi-C: high fidelity Hi-C data simulation for benchmarking and data augmentation

Year: 2019

Type: preprint

Abstract: Ability to simulate realistic high-throughput chromatin conformation (Hi-C) data is foundational for developing and benchmarking statistical and computational methods for Hi-C data analysis. We propose FreeHi-C, a data-driven Hi-C simulator for simulating and augmenting Hi-C datasets. FreeHi-C employs a non-parametric strategy for estimating interaction distribution of genome fragments from a given sample and simulates Hi-C reads from interacting fragments. Data from FreeHi-C exhibit higher fidelity to the biological Hi-C data compared with other tools in its class. FreeHi-C not only enables benchmarking a wide range of Hi-C analysis methods but also boosts the precision and power of differential chromatin interaction detection methods while preserving false discovery rate control through data augmentation.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.1101/629923

Authors: Ye Zheng, Sündüz Keleş

Institution: University of Wisconsin–Madison

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Human Genome Research Institute

Award: Statistical Methods For Annotating Repetitive Genomic Regions Through ENCODE-deri