Last changes to the handouts.

practical_one/practical_one.tex

@@ -19,7 +19,7 @@
 
 \title{NGS Introduction Course\\
   {\Large Practical one, Linux and NGS tools}}
-\date{Tuesday, 1 April 2014}
+\date{Tuesday, April 1, 2014}
 \author{Jeroen Laros, Michiel van Galen}
 
 \begin{document}
@@ -47,12 +47,10 @@ Hints:
 
 % Connect to the VM
 \subsection{Connecting to a machine}
-We will do the practical on a virtual machine in the LUMC. Everything is
-already prepared and ready to use. To connect we use ssh.
-\begin{lstlisting}
-  PUTTY?
-  $ ssh course@0.0.0.0
-\end{lstlisting}
+We will do the practical on a virtual machine at the LUMC. Everything is
+already prepared and ready to use. To connect we use PuTTY, see the
+preparations\footnote{https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/NGS-intro-prep}
+page for instructions on how to install and use it.
 
 % Files and directories
 \subsection{Files and directories}
@@ -365,9 +363,9 @@ less disk space! Let's convert the file.
 \medskip
 
 The first option we need to give Samtools is which function to use, in our
-case we use ``view''. After that we give ``-Sb'', basically telling Samtools that
-our input is SAM and we would like BAM output. Finally we redirect the output
-to a new output file using the greater than sign.
+case we use ``view''. After that we give ``-Sb'', basically telling Samtools
+that our input is SAM and we would like BAM output. Finally we redirect the
+output to a new output file using the greater than sign.
 \medskip
 
 For many purposes it is convenient, and often even required, to have your BAM
@@ -377,8 +375,8 @@ useful. To sort the file, we simply call Samtools sort. The first argument is
 the input file, followed by the output file name.
 \medskip
 
-Note that we omit the .bam extension for the output file name. This will be done
-by Samtools.
+Note that we omit the .bam extension for the output file name. This will be
+done by Samtools.
 \medskip
 
 \begin{itemize}
@@ -403,16 +401,16 @@ Let's continue with calling variants. Again, we make use of the Samtools
 bundle, yet this time we call mpileup. This converts the BAM into a per
 position summary of calls in text format. The size of this can get quite big so
 instead of saving the mpileup file we immediately feed it into bcftools using a
-pipe. We will not go into what the ``-guf'' flag means anymore. If you like, you
-can ``samtools mpileup'' to see what the individual characters mean in this
+pipe. We will not go into what the ``-guf'' flag means anymore. If you like,
+you can ``samtools mpileup'' to see what the individual characters mean in this
 sense. 
 \medskip
 
 As explained, the mpileup data will be fed directly into bcftools. At this
 point bcftools will go over the pileup format, picks out the variants and
-describes them into a bcf file. (A binary format of the vcf format.) In the next
-step we will convert the bcf file to a readable vcf file while at the same time
-we apply a filter step from vcfutils.
+describes them into a bcf file. (A binary format of the vcf format.) In the
+next step we will convert the bcf file to a readable vcf file while at the same
+time we apply a filter step from vcfutils.
 \medskip
 
 \begin{itemize}
@@ -442,8 +440,7 @@ VEP to annotate the variants in our vcf file.
   \item Run the VEP with the suggested options:
 \end{itemize}
 \begin{lstlisting}
-  $ /usr/local/variant_effect_predictor/variant_effect_predictor-71/variant_effect_predictor.pl \
-     -i course.vcf -o course.vep --database
+  $ variant_effect_predictor -i course.vcf -o course.vep --database
 \end{lstlisting}
 \medskip
 

practical_two/practical_two.tex

@@ -19,7 +19,7 @@
 
 \title{NGS Introduction Course\\
   {\Large Practical two, Pipelines}}
-\date{Friday, 4 April 2014}
+\date{Friday, April 4, 2014}
 \author{Jeroen Laros, Michiel van Galen}
 
 \begin{document}