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Commit 8309cac2 authored by Laros's avatar Laros
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Added a presentation.

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[submodule "submodules/presentation"]
path = submodules/presentation
url = https://git.lumc.nl/j.f.j.laros/presentation.git
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\documentclass[slidestop]{beamer}
\title{NGS barcodes}
\providecommand{\myConference}{NGS work discussion}
\providecommand{\myDate}{Wednesday, 5 June 2013}
\author{Jeroen F. J. Laros}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\providecommand{\lastCenterLogo}{
\raisebox{-0.1cm}{
\includegraphics[height = 1cm]{lgtc_logo}
%\includegraphics[height = 0.7cm]{ngi_logo}
}
}
\providecommand{\lastRightLogo}{
%\includegraphics[height = 0.7cm]{nbic_logo}
%\includegraphics[height = 0.8cm]{nwo_logo_en}
%\hspace{1.5cm}\includegraphics[height = 0.7cm]{gen2phen_logo}
}
\usetheme{lumc}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title page.
\bodytemplate
% First page of the presentation.
\section{Introduction}
\begin{frame}
\frametitle{Barcoding}
Idea:
\begin{itemize}
\item Add a sequence to identify a sample.
\begin{itemize}
\item Usually in the adapter.
\end{itemize}
\item Use this sequence to \emph{demultiplex} a dataset.
\end{itemize}
\bigskip
\pause
Characteristics:
\begin{itemize}
\item No ``difficult sequences'':
\begin{itemize}
\item Mononucleotide stretches.
\item \bt{GC}-content.
\end{itemize}
\item Sequencing error correction.
\begin{itemize}
\item A barcode must have a distance of at least $3$ to all others.
\end{itemize}
\end{itemize}
\end{frame}
\begin{frame}
\frametitle{Edit distance (or Levenshtein distance)}
\[
\mathrm{lev}_{a, b}(i, j) =
\begin{cases}
\mathrm{max}(i, j) & \hspace{-2.25cm}\mathrm{if\ min}(i, j) = 0,\\
\mathrm{min}
\begin{cases}
\mathrm{lev}_{a, b}(i - 1, j) + 1\\
\mathrm{lev}_{a, b}(i, j - 1) + 1 & \mathrm{otherwise.}\\
\mathrm{lev}_{a, b}(i - 1, j - 1) + [a_i \neq b_j]\\
\end{cases}
\end{cases}
\]
\bigskip
Allows for insertions, deletions and substitutions.
\bigskip
\pause
Example (distance = 3):
\begin{center}
\bt{%
GATCGGACC-G\\
| |||| || |\\
G-TCGGTCCCG\\
}
\end{center}
\end{frame}
\begin{frame}
\frametitle{Hamming distance}
\[
\mathrm{ham}_{a, b} = \sum_{i = 0}^{|a|} [a_i \neq b_i]
\]
\bigskip
Only allows for substitutions.
\bigskip
\pause
Example (distance = 5):
\begin{center}
\bt{%
GATCGGACCG\\
| \ \ | \ |||\\
GTCGGTCCCG\\
}
\end{center}
\end{frame}
\section{Barcode design}
\begin{frame}[fragile]
\frametitle{The \bt{barcode} package}
Tool kit for:
\begin{itemize}
\item Creating barcodes.
\begin{itemize}
\item Specify length.
\item Maximum mononucleotide stretch length.
\item Minimum distance to other barcodes.
\begin{itemize}
\item Edit distance.
\item Hamming distance.
\end{itemize}
\end{itemize}
\pause
\item Checking barcode lists.
\begin{itemize}
\item Check the distance constraint.
\begin{itemize}
\item Edit distance.
\item Hamming distance.
\end{itemize}
\end{itemize}
\end{itemize}
\bigskip
\pause
\begin{lstlisting}[language=bash]
pip install barcode
\end{lstlisting}
\end{frame}
\section{Checking existing lists}
\begin{frame}
\begin{table}[]
\begin{center}
{\small
\begin{tabular}{lrr}
name & total & removed\\
\hline
FlexSel & 10 & 2\\
MID & 151 & 0\\
MP\_index & 48 & 30\\
NexteraCustom & 12 & 2\\
Nextera & 12 & 2\\
PB & 11 & 1\\
SAGE & 12 & 2\\
smallRNA\_new & 6 & 1\\
smallRNA\_old & 5 & 0\\
SOL-MP-L & 12 & 1\\
SrekNeo & 8 & 0\\
TruSeq & 12 & 2\\
TruSeqSmallRNA & 48 & 14\\
TruSeqUni & 12 & 0\\
\end{tabular}
}
\end{center}
\caption{Bad barcodes based on the edit distance.}
\end{table}
\end{frame}
\begin{frame}
\begin{table}[]
\begin{center}
{\small
\begin{tabular}{lrr}
name & total & removed\\
\hline
FlexSel & 10 & 2\\
MID & 151 & 0\\
MP\_index & 48 & 26\\
NexteraCustom & 12 & 0\\
Nextera & 12 & 0\\
PB & 11 & 0\\
SAGE & 12 & 2\\
smallRNA\_new & 6 & 0\\
smallRNA\_old & 5 & 0\\
SOL-MP-L & 12 & 0\\
SrekNeo & 8 & 0\\
TruSeq & 12 & 0\\
TruSeqSmallRNA & 48 & 1\\
TruSeqUni & 12 & 0\\
\end{tabular}
}
\end{center}
\caption{Bad barcodes based on the Hamming distance.}
\end{table}
\end{frame}
\section{Conclusions}
\begin{frame}
\frametitle{Be careful with barcodes}
Only the ``MID'' set seems to be usable for 454 and Ion Torrent.
\bigskip
\pause
Make sure to use the \emph{Hamming distance} when demultiplexing Illumina
data.
\bigskip
\pause
For the following sets, do not use error correction:
\begin{itemize}
\item FlexSel.
\item MP\_index.
\item SAGE.
\item TruSeqSmallRNA.
\end{itemize}
\bigskip
\bigskip
\pause
Do not mix barcode sets, do not design them yourself.
\end{frame}
\section{Questions?}
\lastpagetemplate
\begin{frame}
\begin{center}
Acknowledgements:
\bigskip
\bigskip
\end{center}
\end{frame}
\end{document}
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presentation @ 4df24322
Subproject commit 4df243224d82c66f7858659e311c2ef67244ba36
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