HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

Yih-Chii Hwang, Chiao-Feng Lin, Otto Valladares, John Malamon, Pavel P. Kuksa, Qi Zheng, Brian D. Gregory, Li-San Wang

Abstract: Summary: We implemented a high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA–DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer–target gene relationships.