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

Title	HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.
Publication Type	Journal Article
Year of Publication	2015
Authors	Hwang, Y-C, Lin, C-F, Valladares, O, Malamon, J, Kuksa, PP, Zheng, Q, Gregory, BD, San Wang, L-
Journal	Bioinformatics
Volume	31
Issue	8
Pagination	1290-2
Date Published	2015 Apr 15
ISSN	1367-4811
Keywords	DNA, Enhancer Elements, Genetic, Humans, Programming Languages, Promoter Regions, Genetic, Sequence Analysis, DNA
Abstract	UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: This software package is designed to run on high-performance computing clusters with Oracle Grid Engine. The source code is freely available under the MIT license for academic and nonprofit use. The source code and instructions are available at the Wang lab website (http://wanglab.pcbi.upenn.edu/hippie/). It is also provided as an Amazon Machine Image to be used directly on Amazon Cloud with minimal installation. CONTACT: lswang@mail.med.upenn.edu or bdgregor@sas.upenn.edu SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.
DOI	10.1093/bioinformatics/btu801
Alternate Journal	Bioinformatics
PubMed ID	25480377
PubMed Central ID	PMC4393516
Grant List	P30 AG010124 / AG / NIA NIH HHS / United States R01 GM099962 / GM / NIGMS NIH HHS / United States R01-GM099962 / GM / NIGMS NIH HHS / United States U24-AG041689 / AG / NIA NIH HHS / United States