Big updates to content

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}
 

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}