More slides

presentation/presentation.tex

@@ -35,23 +35,32 @@
   \tableofcontents
 }
 
-\section{Introduction}
+% Todo:
+% Split read alignment (RNA): Tophat, GSNAP
+% Blast
+% Color space
+% Viewers (IGV, Genome Browser, Savant, GBrowse)
+
+\section{Sequence alignment}
 
 \begin{frame}
-  \frametitle{Topics}
+  \vspace{2em}
+
+  \begin{quote}
+    Identifying regions of similarity in sequences
+  \end{quote}
+
+  \pause
+  \vspace{2em}
+
+  {\bf \em In NGS}
   \begin{itemize}
-    \item BAQ
-    \item Paired end reads
-    \item Split read alignment (RNA): Tophat, GSNAP
-    \item Blast
-    \item Color space
-    \item Viewers (IGV, Genome Browser, Savant, GBrowse)
-    \item \ldots
+    \item Recovering original nucleotide sequence
+    \item \ldots from many short fragments
+    \item \ldots using a known reference
   \end{itemize}
 \end{frame}
 
-\section{Sequence alignment}
-
 \begin{frame}
   \frametitle{Pairwise alignment}
   \begin{center}
@@ -93,6 +102,7 @@
     \includegraphics[width=\textwidth]{assembly}
     % http://cbsu.tc.cornell.edu/ngw2010/day2_lecture1.pdf
   \end{center}
+  \pause
   {\bf \em Alignment}
   \begin{center}
     \includegraphics[width=\textwidth]{alignment}
@@ -109,6 +119,7 @@
     \item Needs high coverage
   \end{itemize}
 
+  \pause
   \vspace{1em}
 
   {\bf \em Alignment}
@@ -154,10 +165,11 @@ A&0&2&3&6&7&10&10&10&12
 \begin{frame}
   \frametitle{2-step alignment}
   \vspace{1em}
+  \only<2>{
   Step 1: Find candidate positions
   \begin{itemize}
     \item Use read seeds
-    \item Hash table-based or burrows Wheeler transform-based heuristic
+    \item Hash table-based or Burrows Wheeler transform-based heuristic
     \item Balance between speed and accuracy
   \end{itemize}
   \vspace{0.5em}
@@ -165,11 +177,8 @@ A&0&2&3&6&7&10&10&10&12
     \includegraphics[width=0.7\textwidth]{seed}
     % http://cbsu.tc.cornell.edu/ngw2010/day2_lecture1.pdf
   \end{center}
-\end{frame}
-
-\begin{frame}
-  \frametitle{2-step alignment}
-  \vspace{1em}
+  }
+  \only<3>{
   Step 2: Align and report
   \begin{itemize}
     \item Complete alignment with Smith-Waterman
@@ -180,6 +189,7 @@ A&0&2&3&6&7&10&10&10&12
     \includegraphics[width=\textwidth]{score}
     % http://cbsu.tc.cornell.edu/ngw2010/day2_lecture1.pdf
   \end{center}
+  }
 \end{frame}
 
 \section{Common problems}
@@ -215,15 +225,16 @@ A&0&2&3&6&7&10&10&10&12
 
 \begin{frame}
   \frametitle{Paired-end sequencing}
-  \begin{itemize}
-    \item Align reads separately
-    \item Choose from non-unique alignments based on pairing
-  \end{itemize}
-  \vspace{1em}
   \begin{center}
     \includegraphics[width=\textwidth]{paired}
     % http://www.pnas.org/content/109/4/1347/F1.expansion.html
   \end{center}
+  \pause
+  \vspace{1em}
+  \begin{itemize}
+    \item Align reads separately
+    \item Choose from non-unique alignments based on pairing
+  \end{itemize}
 \end{frame}
 
 \begin{frame}