From c4b2e96665137dc2650963f07135d27edb28200f Mon Sep 17 00:00:00 2001
From: Michiel van Galen <m.van_galen@lumc.nl>
Date: Wed, 19 Mar 2014 13:23:00 +0100
Subject: [PATCH] Big updates to content
---
analysis_intro/analysis_intro.tex | 51 +++++----
getting_started/getting_started.tex | 154 +++++++++++++++++++++++-----
2 files changed, 161 insertions(+), 44 deletions(-)
diff --git a/analysis_intro/analysis_intro.tex b/analysis_intro/analysis_intro.tex
index 015787f..8c49840 100644
--- a/analysis_intro/analysis_intro.tex
+++ b/analysis_intro/analysis_intro.tex
@@ -29,16 +29,19 @@
% Make the title page.
\bodytemplate
-% First page of the presentation.
+% First page of the presentation
\section{Introduction to NGS data analysis}
\subsection{Introduction to NGS}
\begin{pframe}
- \bigskip
-
- This will be tought in the lectures.
+ An introduction into NGS will be handled in the other lectures.
+ However, tell us any questions you still may have.
+ \begin{figure}
+ \centering
+ \includegraphics[width=0.65\textwidth]{developments-in-ngs}
+ \end{figure}
\end{pframe}
-\subsection{Data}
+\subsection{Introduction to data}
\begin{pframe}
\begin{figure}
\centering
@@ -46,7 +49,7 @@
\end{figure}
\end{pframe}
-\subsection{Analysis}
+\subsection{Introduction to analysis}
\begin{pframe}
\begin{figure}
\centering
@@ -54,27 +57,35 @@
\end{figure}
\end{pframe}
-\subsection{Applications LUMC}
+% Section
+\section{About us and this course}
+\subsection{NGS activities in the LUMC}
\begin{pframe}
+ LGTC, SASC, ServiceXS
+ \begin{itemize}
+ \item Data production and management
+ \item Development and maintainance of analysis pipelines
+ \end{itemize}
+ \bigskip
+
+ Wide range of different aproaches and applications towards multiple purposes:
\begin{itemize}
- \item Develop and maintain pipelines
- \item Data management
- \item Wide range of applications
- \begin{itemize}
- \item Fundamental research
- \item Clinical
- \end{itemize}
+ \item Fundamental research and clinical applications
+ \item Various technologies: HiSeq, MiSeq, Pacbio, Proton, etc.
+ \item Numerous techniques: DNA, RNA, capture, etc.
+ \item Diverse input: Humans, other animals, bacteria, etc.
\end{itemize}
\end{pframe}
-\subsection{Course focus}
+\subsection{This course focus}
\begin{pframe}
+ We will introduce you into the following areas:
\begin{itemize}
- \item Operating systems
- \item Install and maintain your software
- \item Starting analysis
- \item Using computer resources
- \item Pipelines
+ \item Operating systems (Linux)
+ \item Installing and maintaining your software
+ \item Starting NGS analysis
+ \item Using (remote) computer resources
+ \item Analysis pipelines
\end{itemize}
\end{pframe}
diff --git a/getting_started/getting_started.tex b/getting_started/getting_started.tex
index ca4bdb9..b6d429f 100644
--- a/getting_started/getting_started.tex
+++ b/getting_started/getting_started.tex
@@ -36,8 +36,8 @@
\subsection{Overview}
\begin{pframe}
\begin{itemize}
- \item How to work in a terminal
- \item NGS tools
+ \item How to work with Linux
+ \item Working with NGS tools
\bigskip
\item Cheatsheet is available in the course repository
@@ -51,15 +51,15 @@
\item Linux is case sensitive
\item Tab completion: start typing then TAB
\item To end command line execution:
- \begin{itemize}
- \item `ctrl-c'
- \end{itemize}
- \item To show the manual of a command: `man COMMAND'
+ \begin{itemize}
+ \item `ctrl-c'
+ \end{itemize}
+ \item To show the manual of a command: `man COMMAND'
\end{itemize}
\end{pframe}
-% Section.
-\section{Navigation through the filesystem}
+% Section
+\section{Using a terminal}
\subsection{Folder structure}
\begin{pframe}
\begin{itemize}
@@ -67,8 +67,8 @@
\end{itemize}
\begin{figure}
\caption{Tree structure}
- \centering
- \includegraphics[width=0.4\textwidth]{tree}
+ \centering
+ \includegraphics[width=0.4\textwidth]{tree}
\end{figure}
\end{pframe}
@@ -108,6 +108,7 @@
\end{itemize}
\end{pframe}
+\section{Manipulate files}
\subsection{Copy and move}
\begin{pframe}
\begin{itemize}
@@ -192,7 +193,7 @@
\end{lstlisting}
\end{pframe}
-% Section.
+% Section
\section{Streams, piping and redirecting}
\subsection{Redirecting output to files}
\begin{pframe}
@@ -284,7 +285,7 @@
\end{lstlisting}
\end{pframe}
-% Section.
+% Section
\section{Writing a shell script}
\subsection{Do something for each something}
\begin{pframe}
@@ -305,16 +306,16 @@
\begin{pframe}
\begin{itemize}
\item nano - Nano's ANOther editor
- \begin{itemize}
- \item Simple editor, doesn't rely on the mouse
- \item Many useful features, invoked by holding the ctrl key
- \item For example: \string^X Exit means ctrl-x to exit
- \begin{figure}
- \caption{Nano}
- \centering
- \includegraphics[width=0.5\textwidth]{nano.eps}
- \end{figure}
- \end{itemize}
+ \begin{itemize}
+ \item Simple editor, doesn't rely on the mouse
+ \item Many useful features, invoked by holding the ctrl key
+ \item For example: \string^X Exit means ctrl-x to exit
+ \begin{figure}
+ \caption{Nano}
+ \centering
+ \includegraphics[width=0.5\textwidth]{nano.eps}
+ \end{figure}
+ \end{itemize}
\end{itemize}
\end{pframe}
@@ -380,11 +381,116 @@
\end{itemize}
\bigskip
- \item Don't forget the cheat sheet
+ \item Don't forget the cheat sheet!
+ \end{itemize}
+\end{pframe}
+
+% Section NGS
+\section{Working with NGS tools}
+\subsection{Analysis workflow}
+\begin{pframe}
+ For this course we will go over the steps to analyse a human dataset short reads for variants:
+ \smallskip
+ \begin{itemize}
+ \item Quality control
+ \item Quality trimming
+ \item Alignment
+ \item Variant calling
+ \item Annotation
+ \end{itemize}
+ In the practical we will practice how to apply these steps using standard tools
+\end{pframe}
+
+\subsection{Quality control}
+\begin{pframe}
+ \begin{itemize}
+ \item FastQC: A quality control tool for high throughput sequence data.
+ \item Assess the quality of your data in a fastq file
+ \end{itemize}
+ \begin{figure}
+ \caption{Fastqc}
+ \centering
+ \includegraphics[width=0.5\textwidth]{pretrimmed_qscores}
+ \end{figure}
+\end{pframe}
+
+\subsection{Quality trimming}
+\begin{pframe}
+ \begin{itemize}
+ \item Sickle: A windowed adaptive trimming tool for FASTQ files using quality.
+ \item Only maintain the high-quality bases in a given windowsize
+ \item Works on single and paired end
+ \end{itemize}
+ \begin{lstlisting}[language=none, caption={}]
+ @Header
+ ACGTACGTACGT
+ +
+ !#II!JJJI##!
+
+ Will result in:
+ --GTACGTA---
+ \end{lstlisting}
+\end{pframe}
+
+\subsection{Alignment}
+\begin{pframe}
+ \begin{itemize}
+ \item Many, many different tools available
+ \item Input, output, paired end and multi threading are usually supported
+ \item Underlying methods and technical background vary
+ \begin{itemize}
+ \item Gapped or ungapped alignment
+ \item CPU or RAM focus
+ \item Indexing of genome
+ \end{itemize}
+ \item SAM/BAM output is widely adapted and used for many downstream tools
+ \item In the practical we will use Bowtie
+ \end{itemize}
+ \vfill
+ \footnotesize{http://en.wikipedia.org/wiki/List\_of\_sequence\_alignment\_software}
+\end{pframe}
+
+\subsection{Variant calling}
+\begin{pframe}
+ \begin{itemize}
+ \item Multiple options available each with their own pros and cons
+ \begin{itemize}
+ \item GATK pipeline
+ \item Samtools
+ \item Varscan
+ \end{itemize}
+ \item For the practical we will stick to Samtools
+ \end{itemize}
+\end{pframe}
+
+\subsection{Annotation}
+\begin{pframe}
+ \begin{itemize}
+ \item Ensembl, Variant Effect Predictor
+ \begin{itemize}
+ \item On- and offline, different sources, many options
+ \end{itemize}
+ \end{itemize}
+ \begin{figure}
+ \centering
+ \includegraphics[width=1\textwidth]{survey_variant_analysis}
+ \end{figure}
+\end{pframe}
+
+% Last section
+\section{Recap}
+\subsection{Summary}
+\begin{pframe}
+ \begin{itemize}
+ \item You have learned the basics to work in a Linux terminal
+ \item You have gotten an idea of a small selection of NGS tools
+ \bigskip
+
+ \item In the practical you will learn how to use these tools
+ \item This knowledge can be applied to install and use your own tools of choice
\end{itemize}
\end{pframe}
-% Last section.
\section{Questions?}
\lastpagetemplate
\begin{pframe}
--
GitLab