Hwang Yih-Chii, Lin Chiao-Feng, Valladares Otto, Malamon John, Kuksa Pavel P, Zheng Qi, Gregory Brian D, Wang Li-San
Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.
Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 Genomics and Computational Biology Graduate Program, University of Pennsylvania, Institute for Biomedical Informatics, University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.
Bioinformatics. 2015 Apr 15;31(8):1290-2. doi: 10.1093/bioinformatics/btu801. Epub 2014 Dec 4.
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.
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.
lswang@mail.med.upenn.edu or bdgregor@sas.upenn.edu
Supplementary Material is available at Bioinformatics online.
我们实施了一个用于启动子相互作用增强子元件的高通量鉴定流程,以简化从映射原始Hi-C读数、高置信度和质量控制地识别DNA-DNA相互作用片段、检测推定增强子元件中的组蛋白修饰和DNase超敏富集,到最终提取可能的染色体内和染色体间增强子-靶基因关系的工作流程。
此软件包设计用于在配备Oracle网格引擎的高性能计算集群上运行。源代码根据MIT许可免费提供,供学术和非营利使用。源代码和说明可在王实验室网站(http://wanglab.pcbi.upenn.edu/hippie/)获取。它也作为亚马逊机器镜像提供,可在亚马逊云直接使用,安装最少。
lswang@mail.med.upenn.edu或bdgregol@sas.upenn.edu
补充材料可在《生物信息学》在线获取。