|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-|
|Date Published||2015 Apr 15|
|Keywords||DNA, Enhancer Elements, Genetic, Humans, Programming Languages, Promoter Regions, Genetic, Sequence Analysis, DNA|
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: firstname.lastname@example.org or email@example.com
SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.
|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