HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements
| Autor: | Pavel P. Kuksa, Chiao-Feng Lin, John Malamon, Yih-Chii Hwang, Brian D. Gregory, Qi Zheng, Li-San Wang, Otto Valladares |
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| Rok vydání: | 2014 |
| Předmět: |
Statistics and Probability
Source code Sequence analysis Computer science media_common.quotation_subject computer.software_genre Biochemistry Humans Promoter Regions Genetic Enhancer Molecular Biology Gene Throughput (business) media_common Enhancer Elements biology DNA Sequence Analysis DNA Applications Notes Pipeline (software) Computer Science Applications Computational Mathematics Identification (information) Enhancer Elements Genetic Histone Computational Theory and Mathematics Operating system biology.protein Programming Languages Data mining computer |
| Zdroj: | Bioinformatics. 31:1290-1292 |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | 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. 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. |
| Databáze: | OpenAIRE |
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