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\documentclass[xcolor=dvipsnames]{beamer}
\usepackage{BioconductorSlides}
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  \begin{frame}<beamer>{Outline}
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\begin{document}

\title{Read Counting in RNA-seq}

\author{Herv\'e Pag\`es\\
        \href{mailto:hpages@fhcrc.org}{hpages@fhcrc.org}}

\institute[FHCRC]{Fred Hutchinson Cancer Research Center\\
                  Seattle, WA, USA}

\date{21 January 2014}

\maketitle

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\section{Introduction}
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\begin{frame}[fragile]
  \frametitle{The 2 types of applications of RNA-seq}
  \begin{block}{}
    Discovery
    \begin{itemize}
      \item find new transcripts
      \item find transcript boundaries
      \item find splice junctions
    \end{itemize}

    \medskip

    Comparison
    Given samples from different experimental conditions, find effects
    of the treatment on
    \begin{itemize}
      \item gene expression strengths (a.k.a. ``differential analysis at the
            gene level'')
      \item isoform abundance ratios
    \end{itemize}
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Workflow of a differential analysis of RNA-Seq data}
  \begin{block}{}
    \begin{itemize}
      \item Start with: Short-read sequences with qualities (FASTQ files)
      \item Align to a reference genome ==> SAM files
      \item Count reads per gene or exon (based on a gene model) => matrix
            of counts
      \item Statistical analysis on the counts (fold-changes, p values,
            etc...)
      \item Downstream analyses (gene set enrichment analysis, nearest
            peak to a differentially expressed gene, etc...)
    \end{itemize}
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Alignment}
  \begin{block}{}
    Typically done with a stand-alone software.

    For RNA-Seq, we need a splice-aware aligner:
    \begin{itemize}
      \item TopHat2
      \item GSNAP
      \item etc...
    \end{itemize}
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Counting reads per gene}
  \begin{block}{}
    \begin{itemize}
      \item Count each read at most once.
      \item Discard a read if
            \begin{itemize}
              \item it cannot be uniquely mapped
              \item its alignment overlaps with several genes
              \item the alignment quality score is bad
              \item (for paired-end reads) the mates do not map to
                    the same gene
            \end{itemize}
    \end{itemize}
  \end{block}
\end{frame}


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\section{Counting the reads with Bioconductor}
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\begin{frame}[fragile]
  \frametitle{Reading BAM files}
  \begin{block}{}
    TODO...
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Chosing and loading a gene model}
  \begin{block}{}
    TODO...
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Using \Rfunction{summarizeOverlaps}}
  \begin{block}{}
    TODO...
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \frametitle{Basic manipulation of a \Rclass{SummarizedExperiment} object}
  \begin{block}{}
    TODO...
  \end{block}
\end{frame}

\end{document}