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

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 significant, harmonized, queryable, chromatin interactions in a consistent BED-like format across cell/tissue types and CCC assays. Availability CHARMER is freely available at https://bitbucket.org/wanglab-upenn/CHARMER and harmonized chromatin interaction data will be available in the upcoming version of the FILER database ( https://lisanwanglab.org/FILER ).