使用BioWardrobe分析染色质免疫沉淀测序（ChIP-Seq）和RNA测序（RNA-Seq）数据。
Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe.
作者信息
Vallabh Sushmitha, Kartashov Andrey V, Barski Artem
机构信息
Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
出版信息
Methods Mol Biol. 2018;1783:343-360. doi: 10.1007/978-1-4939-7834-2_17.
The massive amount of information produced by ChIP-Seq, RNA-Seq, and other next-generation sequencing-based methods requires computational data analysis. However, biologists performing these experiments often lack training in bioinformatics. BioWardrobe aims to bridge this gap by providing a convenient user interface and by automating routine data-processing steps. This protocol details the use of BioWardrobe for identifying and visualizing ChIP-Seq peaks, calculating RPKMs, performing differential binding or gene expression analysis, and creating plots and heat maps. We specifically describe how to use BioWardrobe's quality control measures for troubleshooting NGS-based experiments.
ChIP-Seq、RNA-Seq和其他基于新一代测序的方法产生了海量信息，这需要进行计算数据分析。然而，进行这些实验的生物学家往往缺乏生物信息学方面的培训。BioWardrobe旨在通过提供便捷的用户界面以及自动化常规数据处理步骤来弥合这一差距。本方案详细介绍了如何使用BioWardrobe来识别和可视化ChIP-Seq峰、计算每百万映射读取中来自目标基因的读取数（RPKM）、进行差异结合或基因表达分析以及创建图表和热图。我们特别描述了如何使用BioWardrobe的质量控制措施来解决基于新一代测序的实验中出现的问题。
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