%% \VignetteIndexEntry{Project Overview—Slides} %% \VignetteEngine{knitr::knitr} \documentclass[xcolor=dvipsnames]{beamer} \ useppackage {BioconductorSlides} \ useppackage [round]{natbib} \hypersetup{colorlinks,linkcolor=，urlcolor=Blue} \AtBeginSection[] {\begin{frame} {Outline} \tableofcontents[currentsection] \end{frame}} < opts_chunk$set(cache=TRUE) @ \begin{document} \title{Counting reads for RNA-seq} \author{Martin T. Morgan \url{mtmorgan@fhcrc.org} \ Fred Hutchinson癌症研究中心\ Seattle, WA，美国}date{25 August 2014} maketitle {frame}{变种RNA-seq} begin{enumerate} item已知的基因差异表达\begin{itemize} item Genes， \Biocpkg{DESeq2}， \Biocpkg{edgeR} item Transcripts \item Exons，\Biocpkg{DEXSeq} \end{itemize} \item Novel transcripts \end{enumerate} \end{frame} \begin{frame}{RNA-seq工作流}\begin{enumerate} \item实验设计——保持简单;复制。项目湿实验室准备-协变量&“批”效应的机会项目测序-配对端有价值的转录水平推断项目对齐-典型的全基因组;项目分析——线性模型(如t检验)适合每个感兴趣的区域;差异表达基因的“顶表”\项目理解—差异表达区域的注释、基因集富集、与其他研究的比较、与其他数据类型的整合\end{enumering} \end{frame} begin{frame}{RNA-seq对齐读取的BAM文件，通常每个样本项一个如何计数?什么是“重叠”?项目使用什么(\Bioconductor)软件? \end{itemize} \item Output: region $\times$ sample matrix of read counts \item \emph{Not} RPKM or other `normalized' measure \end{itemize} \end{frame} \begin{frame}{RNA-seq summary: how to count?} \begin{columns} \column{.5\textwidth} Counting modes\medskip\par \includegraphics[width=\textwidth]{figures/summarizeOverlaps-modes.pdf} \column{.5\textwidth} Counting in \Bioconductor{} \begin{itemize} \item \Biocpkg{GenomicAlignments} \Rfunction{summarizeOverlaps()} -- standard adn customized counting modes \item \Biocpkg{Rsubread} \Rfunction{featureCounts()} -- fast; Linux and Mac only \end{itemize} \end{columns} \end{frame} \end{document}