Spellchecked and updated getting started

getting_started/annotation.png

+../presentation-pics/pics/annotation.png
\ No newline at end of file

getting_started/getting_started.tex

@@ -118,7 +118,7 @@
   \begin{lstlisting}[language=none, caption={Copy and move}]
     $ ls
     original.txt work
-    $ cp orginal.txt another.txt
+    $ cp original.txt another.txt
     $ ls
     another.txt original.txt work
     $ mv original.txt archive.txt
@@ -291,7 +291,7 @@
 \begin{pframe}
   \begin{itemize}
     \item Many times it's helpful to do something for each something
-    \item A simple for-oneliner in bash can help us out
+    \item A simple for-one-liner in bash can help us out
     \item for this in that; do something; done
   \end{itemize}
   \begin{lstlisting}[language=none, caption={For loop}]
@@ -389,7 +389,7 @@
 \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:
+  For this course we will go over the steps to analyze a human dataset short reads for variants:
   \smallskip
   \begin{itemize}
     \item Quality control
@@ -408,7 +408,7 @@
     \item Assess the quality of your data in a fastq file
   \end{itemize}
   \begin{figure}
-    \caption{Fastqc}
+    \caption{FastQC}
     \centering
     \includegraphics[width=0.5\textwidth]{pretrimmed_qscores}
    \end{figure}
@@ -418,7 +418,7 @@
 \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 Only maintain the high-quality bases in a given window size
     \item Works on single and paired end
   \end{itemize}
   \begin{lstlisting}[language=none, caption={}]
@@ -432,6 +432,18 @@
   \end{lstlisting}
 \end{pframe}
 
+\subsection{Alignment}
+\begin{pframe}
+  High troughput mapping of reads to a known reference genome
+  \begin{itemize}
+    \item Allow mismatches
+  \end{itemize}
+  \begin{figure}
+    \centering
+    \includegraphics[width=0.68\textwidth]{varcall}
+  \end{figure}
+\end{pframe}
+
 \subsection{Alignment}
 \begin{pframe}
   \begin{itemize}
@@ -464,6 +476,15 @@
   \end{itemize}
 \end{pframe}
 
+\subsection{Annotation}
+\begin{pframe}
+  Adding some context to your variants greatly benefits the interpretation
+  \begin{figure}
+    \centering
+    \includegraphics[width=1\textwidth]{annotation}
+  \end{figure}
+\end{pframe}
+    
 \subsection{Annotation}
 \begin{pframe}
   \begin{itemize}
@@ -487,8 +508,8 @@
     \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
+    \item In the practical you will learn how to use and combine these tools
+    \item This knowledge can be applied to install and use the tools of your choice
   \end{itemize}
 \end{pframe}
 
@@ -496,7 +517,7 @@
 \lastpagetemplate
 \begin{pframe}
   \begin{center}
-    Acknowledgements:
+    Acknowledgments:
     \bigskip
     \bigskip
     

getting_started/varcall.gif

+../presentation-pics/pics/varcall.gif
\ No newline at end of file