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

TitleHIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.
Publication TypeJournal Article
Year of Publication2015
AuthorsHwang Y-C, Lin C-F, Valladares O, Malamon J, Kuksa PP, Zheng Q, Gregory BD, San Wang L-
JournalBioinformatics
Volume31
Issue8
Pagination1290-2
Date Published2015 Apr 15
ISSN1367-4811
KeywordsDNA, 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.

DOI10.1093/bioinformatics/btu801
Alternate JournalBioinformatics
PubMed ID25480377
PubMed Central IDPMC4393516
Grant ListP30 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