FreeHi-C spike-in simulations for benchmarking differential chromatin interaction detection.

ABSTRACT: High-throughput genome-wide chromatin conformation capture assay (Hi-C) is routinely used to profile long-range genomic interactions and three-dimensional organization of genomes. A key application of Hi-C is the comparative analysis of genomic interactions across different time points, cellular conditions, or multiple stimuli. While operating characteristics of methods for Hi-C data processing such as normalization, pairwise interaction and higher-order organization detection have been relatively well studied, properties of methods for differential chromatin interaction detection are less investigated. We have recently developed FreeHi-C to enable data-driven non-parametric simulations from Hi-C experiments. Here, we extend FreeHi-C with a user/data-driven spike-in module to facilitate co

SUBMITTER: Zheng Y 

PROVIDER: S-EPMC7855360 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature