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presentation/presentation.tex

@@ -29,6 +29,7 @@
 % Make the title page.
 \bodytemplate
 
+% Todo: Include table of contents before every section
 \frame{
   \frametitle{Alignment methods}
   \tableofcontents
@@ -49,6 +50,78 @@
   \end{itemize}
 \end{frame}
 
+\section{Sequence alignment}
+
+\begin{frame}
+  \frametitle{Pairwise alignment}
+  \begin{center}
+    \includegraphics[width=\textwidth]{pairwise}
+    % http://en.wikipedia.org/wiki/Sequence_alignment
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Multiple sequence alignment}
+  \begin{center}
+    \includegraphics[width=\textwidth]{msa}
+    % http://en.wikipedia.org/wiki/Multiple_sequence_alignment
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Global vs local alignment}
+  \begin{center}
+    \includegraphics[width=\textwidth]{global}
+    % http://www.pitt.edu/~mcs2/teaching/biocomp/tutorials/global.html
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Structural alignment}
+  \begin{center}
+    \includegraphics[width=0.7\textwidth]{structural}
+    % http://www.biology-direct.com/content/4/1/30/figure/F3?highres=y
+  \end{center}
+\end{frame}
+
+\section{Assembly vs alignment}
+
+\begin{frame}
+  \vspace{1em}
+  {\bf \em Assembly}
+  \begin{center}
+    \includegraphics[width=\textwidth]{assembly}
+    % http://cbsu.tc.cornell.edu/ngw2010/day2_lecture1.pdf
+  \end{center}
+  {\bf \em Alignment}
+  \begin{center}
+    \includegraphics[width=\textwidth]{alignment}
+    % http://cbsu.tc.cornell.edu/ngw2010/day2_lecture1.pdf
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \vspace{1em}
+
+  {\bf \em Assembly}
+  \begin{itemize}
+    \item Memory hungry
+    \item Needs high coverage
+  \end{itemize}
+
+  \vspace{1em}
+
+  {\bf \em Alignment}
+  \begin{itemize}
+    \item Easy to do in parallel
+    \item Restricted by reference sequence
+      \begin{itemize}
+        \item highly polymorphic regions
+        \item large insertions
+      \end{itemize}
+  \end{itemize}
+\end{frame}
+
 \section{Alignment methods}
 
 \begin{frame}[fragile]
@@ -109,120 +182,59 @@ A&0&2&3&6&7&10&10&10&12
   \end{center}
 \end{frame}
 
+\section{Common problems}
 
 \begin{frame}
-  \frametitle{Sequence alignment types}
-
-  \vspace{1em}
-
-  Pairwise alignment\\
-  {\em vs}\\
-  Multiple sequence alignment (MSA)
-
-  \vspace{1em}
-
-  Global alignment\\
-  {\em vs}\\
-  Local alignment
-
-  \vspace{1em}
-
-  One-dimensional sequence alignment\\
-  {\em vs}\\
-  Structural alignment
-\end{frame}
-
-\begin{frame}
-  \frametitle{Pairwise alignment}
-  \begin{center}
-    \includegraphics[width=\textwidth]{pairwise}
-    % http://en.wikipedia.org/wiki/Sequence_alignment
-  \end{center}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Multiple sequence alignment}
-  \begin{center}
-    \includegraphics[width=\textwidth]{msa}
-    % http://en.wikipedia.org/wiki/Multiple_sequence_alignment
-  \end{center}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Global vs local alignment}
-  \begin{center}
-    \includegraphics[width=\textwidth]{global}
-    % http://www.pitt.edu/~mcs2/teaching/biocomp/tutorials/global.html
-  \end{center}
-\end{frame}
-
-\begin{frame}
-  \frametitle{Alignment of NGS reads}
-  Many pairwise one-dimensional sequence alignments
-
-  \vspace{1em}
-
-  Can be global or local w.r.t. the read
-
+  \frametitle{Insertions and deletions (indels)}
+  \begin{itemize}
+    \item Local realignment around indels
+    \item Per-Base Alignment Qualities (BAQ)
+  \end{itemize}
+  \vspace{0.8em}
   \begin{center}
-    \includegraphics[width=\textwidth]{ngs}
-    % GoNL mtDNA in IGV
+    \includegraphics[width=0.8\textwidth]{indel}
+    % GoNL mtDNA alignment
   \end{center}
 \end{frame}
 
 \begin{frame}
-  \frametitle{Platform specifics}
-
+  \frametitle{Non-unique alignment}
+  How to report non-unique alignments?
   \begin{itemize}
-    \item Paired-end sequencing
-    \item Color-space sequencing
-    \item Error profile
+    \item Discard entirely
+    \item Choose one randomly
+    \item Report all
+      \begin{itemize}
+        \item with best quality
+        \item above some quality
+      \end{itemize}
   \end{itemize}
 \end{frame}
 
+\section{Platform specifics}
+
 \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}
 \end{frame}
 
-\section{Assembly vs alignment}
-
-\begin{frame}
-  \vspace{1em}
-  {\bf \em Assembly}
-  \begin{center}
-    \includegraphics[width=\textwidth]{assembly}
-    % http://cbsu.tc.cornell.edu/ngw2010/day2_lecture1.pdf
-  \end{center}
-  {\bf \em Alignment}
-  \begin{center}
-    \includegraphics[width=\textwidth]{alignment}
-    % http://cbsu.tc.cornell.edu/ngw2010/day2_lecture1.pdf
-  \end{center}
-\end{frame}
+\section{Todo}
 
 \begin{frame}
-  \vspace{1em}
-
-  {\bf \em Assembly}
-  \begin{itemize}
-    \item Memory hungry
-    \item Needs high coverage
-  \end{itemize}
-
-  \vspace{1em}
+  \frametitle{Platform specifics}
 
-  {\bf \em Alignment}
   \begin{itemize}
-    \item Easy to do in parallel
-    \item Restricted by reference sequence
-      \begin{itemize}
-        \item highly polymorphic regions
-        \item large insertions
-      \end{itemize}
+    \item Paired-end sequencing
+    \item Color-space sequencing
+    \item Error profile
   \end{itemize}
 \end{frame}
 
@@ -230,14 +242,6 @@ A&0&2&3&6&7&10&10&10&12
   \frametitle{Alignment file formats}
 \end{frame}
 
-\begin{frame}
-  \frametitle{Non-unique alignment}
-  Report none
-  Report all above some quality
-  Report all with best quality
-  Report one randomly
-\end{frame}
-
 \end{document}
 
 % http://lh3lh3.users.sourceforge.net/NGSalign.shtml