Added links to html output

practical_one/practical_one.tex

@@ -305,6 +305,13 @@ This will create a folder with data and plots of the analysis. Have a look at
 the fastq\_data.txt file to get an idea of the metrics of this set of reads. 
 \medskip
 
+FastQC also generates an HTML file. We have put the output somewhere online 
+already for you. In your browser visit the next url:
+\medskip
+
+https://barmsijs.lumc.nl/NGS-course/course.fq\_fastqc/fastqc\_report.html
+\medskip
+
 % Alignment
 \subsection{Alignment with Bowtie}
 We skip the clipping process and continue with the alignment. Run Bowtie, same
@@ -345,7 +352,7 @@ arguments come first before the others. (As you can see in the help)
   \item Run a Bowtie analysis on the data by aligning to the mtDNA index:
 \end{itemize}
 \begin{lstlisting}
-  $ bowtie -S ./ref/chrM course.fq course.sam
+  $ bowtie -S ./bowtie_index/chrM course.fq course.sam
 \end{lstlisting}
 \medskip
 
@@ -446,6 +453,13 @@ same time expand annotation for interesting variants only. Manage this using
 the next parameters.
 \medskip
 
+Like FastQC, VEP also creates an HTML file. We have put this online for you. If
+you like to have a look at this, open a browser and visit:
+\medskip
+
+https://barmsijs.lumc.nl/NGS-course/course.fq.vep\_summary.html
+\medskip
+
 \begin{itemize}
   \item Try some of these parameters and figure out what they do:
   \item -{}-check\_existing -{}-canonical -{}-coding\_only -{}-force\_overwrite