Updated pipeline lecture.

combining_tools/combining_tools.tex

 \documentclass[slidestop]{beamer}
 
 \title{Combining tools into a pipeline}
-\providecommand{\myConference}{NGS Introduction Course}
-\providecommand{\myDate}{Friday, April 4, 2014}
+\providecommand{\myConference}{NGS data analysis, 8th edition}
+\providecommand{\myDate}{Monday, September 1, 2014}
 \author{Jeroen F. J. Laros}
 \providecommand{\myGroup}{Leiden Genome Technology Center}
 \providecommand{\myDepartment}{Department of Human Genetics}
@@ -38,7 +38,6 @@
       \includegraphics[height=0.85\textheight]{pipeline}
     \end{center}
     \caption{A real-life pipeline.}
-    \label{}
   \end{figure}
 \end{pframe}
 
@@ -48,7 +47,6 @@
       \includegraphics[height=0.85\textheight]{assemblyline}
     \end{center}
     \caption{Scene from ``Modern times''.}
-    \label{}
   \end{figure}
 \end{pframe}
 
@@ -175,7 +173,6 @@
       \includegraphics[height=0.85\textheight]{pretrimmed_qscores}
     \end{center}
     \caption{Quality score per position.}
-    \label{}
   \end{figure}
 \end{pframe}
 
@@ -186,7 +183,6 @@
       \includegraphics[height=0.85\textheight]{linker-clip}
     \end{center}
     \caption{Sequencing linkers.}
-    \label{}
   \end{figure}
 \end{pframe}
 
@@ -195,7 +191,7 @@
   Depending on the sequencing platform, parts of the reads need to be removed.
   \begin{itemize}
     \item Remove linker sequences (\emph{Cutadapt}, \emph{FASTX toolkit}).
-    \item Clip low quality reads at the end of the read (\emph{Sickle},
+    \item Trim low quality reads at the end of the read (\emph{Sickle},
       \emph{Trimmomatic}, \emph{FASTX toolkit}).
     \item Length filtering (\emph{Fastools}).
   \end{itemize}
@@ -205,9 +201,9 @@
   The \emph{FastQC toolkit} can be used for quality control (both before and
   after the data cleaning step).
   \begin{itemize}
-    \item GC content.
+    \item Positional nucleotide content.
     \item GC distribution.
-    \item Quality scores distribution.
+    \item Sequence quality distribution.
     \item \ldots
   \end{itemize}
 \end{pframe}
@@ -217,14 +213,14 @@
   \begin{figure}
     \includegraphics[width=\textwidth, height=0.35\textheight]
       {per_base_sequence_content}
-     \caption{Per base sequence content.}
+     \caption{Positional nucleotide content.}
   \end{figure}
-  \vspace{-0.5cm}
+  \vspace{-0.7cm}
 
   \begin{figure}
     \includegraphics[width=\textwidth, height=0.35\textheight]
       {per_sequence_quality}
-    \caption{Per sequence quality.}
+    \caption{Sequence quality distribution.}
   \end{figure}
 \end{pframe}
 
@@ -237,10 +233,7 @@
 
   Not all aligners can deal with indels.
   \begin{itemize}
-    \item Only a couple of years ago, only SNPs were considered.
-    \begin{itemize}
-      \item \emph{Bowtie}.
-    \end{itemize}
+    \item Older aligners only allowed substitutions.
   \end{itemize}
   \medskip
   \pause
@@ -272,7 +265,6 @@
       \includegraphics[width=0.9\textwidth]{varcall}
     \end{center}
     \caption{Result of an alignment.}
-    \label{}
   \end{figure}
 \end{pframe}
 
@@ -464,10 +456,9 @@
 
     Michiel van Galen
 
-    Jeroen Laros
-  \end{center}
+    Martijn Vermaat
 
-  \vfill
-  \permfoot{https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/NGS-intro}
+    Johan den Dunnen
+  \end{center}
 \end{pframe}
 \end{document}