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Laros
lectures
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913e5b5c
Commit
913e5b5c
authored
Mar 04, 2015
by
Laros
Browse files
Updated lab-oriented NGS introduction.
parent
dc795f49
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lectures/intro_bio_ngs/intro_bio_ngs.tex
View file @
913e5b5c
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@@ -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}
...
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@@ -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
{
F
lowcell.
}
\caption
{
HiSeq f
lowcell.
}
\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.
5
cm
}
\vspace
{
-0.
7
cm
}
\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=0.8
8
\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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