Updated Combining Tools presentation.

combining_tools/Ion_Proton_s.jpg

+../.submodules/presentation-pics/pics/Ion_Proton_s.jpg
\ No newline at end of file

combining_tools/combining_tools.tex

 \documentclass[slidestop]{beamer}
-\input{../shared/variables.tex}
 
 \title{Combining tools into a pipeline}
-\providecommand{\myConference}{\courseTitle}
-\providecommand{\myDate}{\dayTwo, \courseYear}
+\providecommand{\myConference}{NGS data analysis, 9th edition}
+\providecommand{\myDate}{Monday, September 28, 2015}
 \author{Jeroen F.J. Laros}
 \providecommand{\myGroup}{Leiden Genome Technology Center}
 \providecommand{\myDepartment}{Department of Human Genetics}
 \providecommand{\myCenter}{Center for Human and Clinical Genetics}
 \providecommand{\lastCenterLogo}{
   \raisebox{-0.1cm}{
-    \includegraphics[height=1cm]{logos/\sponsorOne_logo}
+    \includegraphics[height=1cm]{logos/lgtc_logo}
     %\includegraphics[height = 0.7cm]{ngi_logo}
   }
 }
@@ -95,12 +94,12 @@
   These regions are then \emph{sequenced}.
 \end{pframe}
 
-\subsection{Sequencers: HiSeq}
+\subsection{Illumina}
 \begin{pframe}
   \begin{minipage}[t]{0.47\textwidth}
     \begin{figure}
       \includegraphics[width=\textwidth]{hiseq_2000}
-      \caption{HiSeq 2000.}
+      \caption{HiSeq 2500.}
     \end{figure}
   \end{minipage}
   \hfill
@@ -110,19 +109,19 @@
       \item High throughput.
       \item Paired end.
       \item High accuracy.
-      \item Read length $2 \times 150$bp.
-      \item Relatively long run time.
+      \item Read length $2 \times 125$bp.
+      \item Relatively long run time (6 days).
       \item Relatively expensive.
     \end{itemize}
   \end{minipage}
 \end{pframe}
 
-\subsection{Sequencers: Ion Torrent}
+\subsection{Life Technologies}
 \begin{pframe}
   \begin{minipage}[t]{0.47\textwidth}
     \begin{figure}
-      \includegraphics[width=\textwidth]{ion-torrent}
-      \caption{Ion torrent.}
+      \includegraphics[width=\textwidth]{Ion_Proton_s}
+      \caption{Ion proton.}
     \end{figure}
   \end{minipage}
   \hfill
@@ -142,26 +141,21 @@
 \subsection{Data analysis}
 \begin{pframe}
   Resequencing pipelines can roughly be divided in five steps.
-  \pause
   \begin{enumerate}
     \item Pre-alignment.
     \begin{itemize}
       \item Quality control.
       \item Data cleaning.
     \end{itemize}
-    \pause
     \item Alignment.
     \begin{itemize}
       \item Post-alignment quality control.
     \end{itemize}
-    \pause
     \item Variant calling.
-    \pause
     \item Filtering.
     \begin{itemize}
       \item Post-variant calling quality control.
     \end{itemize}
-    \pause
     \item Annotation.
   \end{enumerate}
 \end{pframe}
@@ -253,7 +247,7 @@
 
   The choice of aligner may be restricted by the sequencer.
   \begin{itemize}
-    \item For the Ion Torrent: \emph{Tmap}.
+    \item For the Ion Torrent / Proton: \emph{Tmap}.
     \item For the PacBio: \emph{BLASR}.
   \end{itemize}
 \end{pframe}
@@ -331,44 +325,57 @@
   \bigskip
   \pause
 
-  A good way to calculate the maximum:
+  A reasonable way to calculate the maximum:
+  \begin{itemize}
+    \item $2.5$ times the average coverage of the targeted regions.
+  \end{itemize}
+  \bigskip
+  \pause
+
+  A better way:
+  \begin{itemize}
+    \item Do CNV calling and use this as a filter.
+  \end{itemize}
+\end{pframe}
+
+\section{Annotation}
+\subsection{Effect prediction}
+\begin{pframe}
+  In most cases we have too many variants.
+  \bigskip
+
+  Variant annotation.
   \begin{itemize}
-    \item Calculate the mean coverage.
+    \item Frequency within a population.
+    \item Location of the variant.
     \begin{itemize}
-      \item Only of the covered (targeted) regions.
+      \item Gene panels.
+      \item Location within a gene.
     \end{itemize}
-    \item Multiply this number with a reasonable factor e.g., $2.5$.
+    \item Conservation.
   \end{itemize}
 \end{pframe}
 
-\section{Annotation}
-\subsection{What is already known about a variant}
+\subsection{Variant Effect Predictor}
 \begin{pframe}
-  A selection of SeattleSeq annotation:
+  A selection of VEP annotation:
   \begin{itemize}
-    \item Is the variant known?
-    \item Does it hit a gene?
-    \pause
+    \item Affected genes and transcripts.
+    \item Location of the variant.
     \begin{itemize}
-      \item Is it in an intron?
-      \begin{itemize}
-        \item Does it hit a splice site?
-      \end{itemize}
-      \pause
-      \item Is it in the coding region?
-      \begin{itemize}
-        \item Is there a gain/loss of a stop codon?
-        \item Does the variant result in a frameshift?
-        \item \ldots
-      \end{itemize}
-      \pause
-      \item Is it in the 5'/3' UTR of a gene?
-      \item \ldots
+      \item Upstream of a transcript, in coding sequence, in non-coding RNA,
+        in regulatory region.
     \end{itemize}
-    \pause
-    \item Is it in a regulatory region?
-    \item \ldots
+    \item Consequence on the protein sequence.
+    \begin{itemize}
+      \item Stop gained, missense, stop lost, frameshift.
+    \end{itemize}
+    \item Minor allele frequencies from the 1000 Genomes Project.
+    \item SIFT and PolyPhen scores for changes to protein sequence.
   \end{itemize}
+
+  \vfill
+  \permfoot{\url{http://www.ensembl.org/info/docs/tools/vep/index.html}}
 \end{pframe}
 
 \section{Pipelines}
@@ -438,25 +445,19 @@
   \end{figure}
 \end{pframe}
 
-\begin{pframe}
-  \begin{figure}
-    \includegraphics[trim=320 0 100 70, clip, width=\textwidth,
-      height=0.9\textheight]{gapss3}
-    \caption{Zoomed in.}
-  \end{figure}
-\end{pframe}
-
 \section{Questions?}
 \lastpagetemplate
 \begin{pframe}
   \begin{center}
+    Acknowledgements:
     \bigskip
     \bigskip
 
-    \acknowledgements
-  \end{center}
+    Martijn Vermaat
 
-  \vfill
-  \permfoot{\courseWebsite}
+    Michiel van Galen
+
+    Johan den Dunnen
+  \end{center}
 \end{pframe}
 \end{document}

combining_tools/ion-torrent.jpg

-../.submodules/presentation-pics/pics/ion-torrent.jpg
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combining_tools/lumc_logo_small.eps

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combining_tools/nwo_logo_en.eps

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combining_tools/nwo_logo_nl.eps

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