CHARMER: detecting and harmonizing high-confidence chromatin interactions across tissues and Hi-C protocols.

ABSTRACT:

Motivation

Chromatin conformation capture experiments (CCC), such as Hi-C and Capture Hi-C (CHiC) work to elucidate the three-dimensional organization of the genome and the underlying epigenetic regulatory structures within. CCC experiments produce large amounts of FASTQ sequencing data with a substantial amount of technical noise and require sophisticated computational pipelines in order to extract meaningful results. Large-scale CCC data repositories like 4D Nucleome and ENCODE mostly provide raw contact information but lack annotated, statistically significant interaction data suitable for downstream genetic and genomic analyses.

Results

Here, we present CHARMER, an end-to-end pipeline integrated across multiple CCC assay types (HiC, CHiC) which generates statistically si

SUBMITTER: Cole S 

PROVIDER: S-EPMC11623617 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature