%\VignetteIndexEntry{Quality assessment}
%\VignettePackage{EMBL2011}

\documentclass{article}

\usepackage{BioconductorVignette}

\title{Quality assessment and remediation}
\author{Martin
  Morgan\footnote{\href{mailto:mtmorgan@fhcrc.org}{mtmorgan@fhcrc.org}}}
\date{June 20-23, 2011}

\SweaveOpts{keep.source=TRUE}

\begin{document}

\maketitle

\section{Opportunities for quality assessment}

Sequences

Alignment

Limitations: not 454 flows, SOLiD

\section{Quality assessment}
  
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

\subsection{Sequence quality assessment}

counts, abc's (by cycle), frequent sequences

\subsection{Alignment quality assessment}

Alignment
- fraction aligning
- strandedness
- alignment scores


RNAseq
- on-target
- insert size
- systematic bias, e.g., 5'$\rightarrow$3'
- mapability

ChIPseq

Variant calls
- depth of coverage

\section{Remediation}

Sequences
- removal
- trimming
- paired-end issues

Alignments
- statistical approaches (models)

\end{document}