Commit 913e5b5c authored by Laros's avatar Laros
Browse files

Updated lab-oriented NGS introduction.

parent dc795f49
......@@ -64,21 +64,6 @@
\end{minipage}
\end{pframe}
%\begin{pframe}
% \begin{minipage}[t]{0.47\textwidth}
% \begin{figure}[]
% \begin{center}
% \includegraphics[width=\textwidth]{cromossomo_descondensando}
% \end{center}
% \caption{Chromosomes.}
% \end{figure}
% \end{minipage}
% \hfill
% \begin{minipage}[t]{0.47\textwidth}
% The nucleus contains \emph{chromosomes}.
% \end{minipage}
%\end{pframe}
\subsection{DNA}
\begin{pframe}
\begin{figure}[]
......@@ -101,15 +86,6 @@
\end{figure}
\end{pframe}
%\begin{pframe}
% \begin{figure}[]
% \begin{center}
% \includegraphics[width=\textwidth]{Simple_transcription_elongation1}
% \end{center}
% \caption{RNA synthesis.}
% \end{figure}
%\end{pframe}
\section{Sequencing}
\subsection{DNA synthesis}
\begin{pframe}
......@@ -173,7 +149,7 @@
Labelled:
\begin{itemize}
\item Optical platform.
\item In system amplification.
\item In system amplification to get enough signal.
\end{itemize}
\bigskip
......@@ -196,6 +172,13 @@
\end{minipage}
\hfill
\begin{minipage}[t]{0.47\textwidth}
In general:
\begin{itemize}
\item Fragmentation.
\item Adapter ligation.
\end{itemize}
\bigskip
Y-adapters:
\begin{itemize}
\item No loss of sample.
......@@ -210,10 +193,13 @@
\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[width=\textwidth]{nextera}
\includegraphics[height=0.6\textheight]{nextera}
\end{center}
\caption{Fragmentation and adapter ligation in one.}
\caption{Nextera.}
\end{figure}
Fragmentation and adapter ligation in one step using a \emph{transposon}
based method.
\end{pframe}
\begin{pframe}
......@@ -227,20 +213,23 @@
\end{minipage}
\hfill
\begin{minipage}[t]{0.47\textwidth}
Capture \emph{coding regions} only.
Capture \emph{coding regions}.
\begin{itemize}
\item About $2\%$ of the genome.
\item Price reduction.
\item Diagnostics.
\end{itemize}
\end{minipage}
\end{pframe}
\subsection{Clustering}
\begin{pframe}
\begin{minipage}[t]{0.47\textwidth}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.88\textheight]{flowcell_2000}
\end{center}
\caption{Flowcell.}
\caption{HiSeq flowcell.}
\end{figure}
\end{minipage}
\hfill
......@@ -295,6 +284,7 @@
\end{minipage}
\end{pframe}
\subsection{Base calling}
\begin{pframe}
\begin{figure}[]
\begin{center}
......@@ -304,57 +294,7 @@
\end{figure}
\end{pframe}
%\begin{pframe}
% \begin{minipage}[t]{0.47\textwidth}
% \begin{figure}[]
% \begin{center}
% \includegraphics[width=0.8\textwidth, height=0.3\textheight]
% {k_flowcell}
% \end{center}
% \caption{Flowcell.}
% \end{figure}
% \vspace{-1cm}
% \begin{figure}[]
% \begin{center}
% \includegraphics[width=0.8\textwidth]{k_bridge2}
% \end{center}
% \caption{Amplification.}
% \end{figure}
% \end{minipage}
% \hfill
% \pause
% \begin{minipage}[t]{0.47\textwidth}
% Optical system.
% \begin{itemize}
% \item DNA fragments are loaded on a flowcell.
% \item Fragments are amplified.
% \item Clusters of fragments give the same signal.
% \end{itemize}
% \end{minipage}
%\end{pframe}
%
%\begin{pframe}
% \begin{minipage}[t]{0.47\textwidth}
% \begin{figure}[]
% \begin{center}
% \includegraphics[trim=0 0 0 5cm, clip, height=0.9\textheight]{paired_end_2}
% \end{center}
% \caption{Paired end.}
% \end{figure}
% \end{minipage}
% \hfill
% \pause
% \begin{minipage}[t]{0.47\textwidth}
% Advantages:
% \begin{itemize}
% \item Mapping to non-unique regions.
% \item Structural variation.
% \item \textit{De novo} assembly (scaffolding).
% \end{itemize}
% \end{minipage}
%\end{pframe}
%
\subsection{Life-Tech}
\subsection{Life-Tech platforms}
\begin{pframe}
\begin{minipage}[t]{0.47\textwidth}
\begin{figure}
......@@ -397,6 +337,24 @@
\end{minipage}
\end{pframe}
\begin{pframe}
These systems use \emph{unlabelled} and \emph{non-blocked} nucleotides.
\bigskip
Unlabelled:
\begin{itemize}
\item Platform measures pH values.
\item Bead amplification to get enough signal.
\end{itemize}
\bigskip
Non-blocked:
\begin{itemize}
\item Only one nucleotide per \emph{flow}.
\item Variable read length.
\end{itemize}
\end{pframe}
\begin{pframe}
\begin{minipage}[t]{0.47\textwidth}
\begin{figure}[]
......@@ -586,7 +544,7 @@
{per_base_sequence_content}
\caption{Per base sequence content.}
\end{figure}
\vspace{-0.5cm}
\vspace{-0.7cm}
\begin{figure}
\includegraphics[width=\textwidth, height=0.35\textheight]
......@@ -601,7 +559,7 @@
\begin{minipage}[t]{0.45\textwidth}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.88\textheight]{k_align}
\includegraphics[height=0.8\textheight]{k_align}
\end{center}
\caption{Visualisation of an alignment.}
\end{figure}
......@@ -849,128 +807,25 @@
\end{figure}
\end{pframe}
%\section{Pipelines}
%\subsection{Pipelines}
%\begin{pframe}
% \begin{figure}[]
% \begin{center}
% \includegraphics[height=0.85\textheight]{pipeline}
% \end{center}
% \caption{A real-life pipeline.}
% \end{figure}
%\end{pframe}
%
%\begin{pframe}
% \begin{figure}[]
% \begin{center}
% \includegraphics[height=0.85\textheight]{assemblyline}
% \end{center}
% \caption{Scene from ``Modern times''.}
% \end{figure}
%\end{pframe}
%
%\begin{pframe}
% Combining tools:
% \begin{itemize}
% \item The output of one tool can serve as the input for another.
% \item Not necessarily linear.
% \item \ldots
% \end{itemize}
% \bigskip
% \pause
%
% Running various different tools:
% \begin{itemize}
% \item Two or three different aligners.
% \item A couple of variant callers.
% \item \ldots
% \end{itemize}
%\end{pframe}
%
%\subsection{Combining tools}
%\begin{pframe}
% \begin{lstlisting}[language=bash, caption=Shell script]
% bwa aln -t 8 $reference $i > $i.sai
% bwa samse $reference $i.sai $i > $i.sam
% samtools view -bt $reference -o $i.bam $i.sam
% \end{lstlisting}
% \medskip
% \pause
%
% \begin{lstlisting}[language=make, caption=Makefile]
% %.sai: %.fq
% $(BWA) aln -t $(THREADS) $(call MKREF, $@) $< > $@
%
% %.sam: %.sai %.fq
% $(BWA) samse $(call MKREF, $@) $^ > $@
%
% %.bam: %.sam
% $(SAMTOOLS) view -bt $(call MKREF, $@) -o $@ $<
% \end{lstlisting}
%\end{pframe}
%
%\section{Graphical interfaces}
%\subsection{Galaxy}
%\begin{pframe}
% Galaxy: a graphical user interface:
% \begin{itemize}
% \item Wrapper for command line utilities.
% \item User friendly.
% \item Point and click.
% \pause
% \item Workflows.
% \begin{itemize}
% \item Save all the steps you did in your analysis.
% \item Rerun the entire analysis on a new dataset.
% \item Share your workflow with other people.
% \item \ldots
% \end{itemize}
% \end{itemize}
%
% \vfill
% \permfoot{http://galaxy.psu.edu/}
%\end{pframe}
%
%\begin{pframe}
% \begin{figure}
% \includegraphics[trim=0 0 0 2cm, clip, width=\textwidth]{galaxy}
% \caption{Galaxy main user interface}
% \end{figure}
%\end{pframe}
%
%\begin{pframe}
% \begin{figure}
% \includegraphics[width=\textwidth, height=0.9\textheight]{galaxy_mpileup}
% \caption{User friendly interface with Galaxy}
% \end{figure}
%\end{pframe}
%
%\subsection{Workflow of a parallel pipeline}
%\begin{pframe}
% \begin{figure}
% \includegraphics[width=\textwidth, height=0.9\textheight]{gapss3}
% \caption{Dependency diagram.}
% \end{figure}
%\end{pframe}
%
%\begin{pframe}
% \begin{figure}
% \includegraphics[trim=320 0 100 70, clip, width=\textwidth,
% height=0.9\textheight]{gapss3}
% \caption{Zoomed in.}
% \end{figure}
%\end{pframe}
\section{Notes}
\subsection{Please remember}
\begin{pframe}
We only covered two systems.
There are many more NGS systems:
\begin{itemize}
\item PacBio RSII.
\item Roche 454.
\item ABI SOLiD.
\end{itemize}
\bigskip
We only covered a few applications.
Other applications:
\begin{itemize}
\item \emph{De novo} assembly.
\item RNA sequencing.
\end{itemize}
\bigskip
We only gave an outline of the data analysis of this selection.
We only gave an outline of the data analysis.
\end{pframe}
\section{Questions?}
......
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