Younesy Hamid, Möller Torsten, Heravi-Moussavi Alireza, Cheng Jeffrey B, Costello Joseph F, Lorincz Matthew C, Karimi Mohammad M, Jones Steven J M
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada, Graphics Usability and Visualization Lab, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada, Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria, Department of Dermatology, University of California San Francisco, San Francisco, California 94143, USA, Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA and Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
Bioinformatics. 2014 Apr 15;30(8):1172-1174. doi: 10.1093/bioinformatics/btt744. Epub 2013 Dec 26.
The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data.
The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea CONTACT: : mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.
使用基于测序的方法评估表达和表观基因组状态，为识别等位基因差异并将其与表观基因组状态相关联提供了前所未有的机会。我们展示了ALEA，这是一个用于等位基因特异性表观基因组学分析的计算工具箱，它将等位基因变异数据整合到现有资源中，从而能够识别表观遗传修饰与人类和小鼠细胞中特定等位基因变体之间的显著关联。ALEA为下一代测序数据（ChIP-seq、RNA-seq等）的等位基因特异性分析提供了一个可定制的命令行工具管道，该管道接收原始测序数据并生成单独的等位基因轨迹，可在基因组浏览器上查看。该管道已通过人类和杂交小鼠的ChIP-seq和RNA-seq数据进行了验证。
该软件包、测试数据和使用说明可在http://www.bcgsc.ca/platform/bioinfo/software/alea在线获取。
mkarimi1@interchange.ubc.ca或sjones@bcgsc.ca
补充数据可在《生物信息学》在线获取。
