Finalized practical one

practical_one/practical_one.tex

@@ -243,8 +243,8 @@ To quickly count how many processes are running we pipe the output to
 % NGS analysis
 \section{NGS analysis}
 We continue this practical on how to use a selection of tools to analyze a
-small human short read dataset. The data will be inpected for quality, aligned,
-checked for variants and annotate these.
+small human short read dataset. The data will be inspected for quality, aligned,
+checked for variants and annotated.
 \medskip
 
 % Copy files
@@ -253,7 +253,8 @@ First we must fetch the course data for the practicals. We have precompiled a
 small human test set of short reads in an online repository. Use the next
 command to pull eveything from that repository for you to work with.
 \medskip 
-How this exactly works is not important for now but if things works as
+
+How this exactly works is not important for now but if things work as
 expected, you should have a folder called ngs-intro-course at the location you
 executed the command. Inside that folder you can find an ``exercise'' folder,
 providing everything you need to continue.
@@ -270,7 +271,7 @@ providing everything you need to continue.
 % Quality control
 \subsection{Quality control with Fastqc}
 Every tool which is systemwide available can simply be run by typing the name
-of the tool.  Try typing part of the toolname and hit TAB twice. It will
+of the tool. Try typing part of the toolname and hit TAB twice. It will
 automatically autocomplete the name or give suggestions if it's not sure yet.
 \medskip
 
@@ -364,10 +365,11 @@ to a new outputfile using the greater than sign.
 
 For many purposes it is convenient, and often even required, to have your BAM
 file sorted. This allows tools only have to go through the file only once.
-Think of an unsorted BAM file as a novel with unsorted pages. To sort the file,
-we simply call Samtools sort. The first argument is the input file, followed by
-the output file name.
+Think of an unsorted BAM file as a novel with unsorted pages, not really
+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 filename. This will be done
 by Samtools.
 \medskip
@@ -386,7 +388,8 @@ by Samtools.
 \subsection{Variant calling with Samtools}
 We have our reads aligned and nicely stowed in a sorted BAM file. This is
 usually the point from where the analysis forks of into different downstream
-analyses. It is a good idea to store and backup your BAM files.
+analyses. It is a good idea to store and backup your BAM files for the projects
+you work on.
 \medskip
 
 Let's continue with calling variants. Again, we make use of the Samtools
@@ -418,6 +421,7 @@ we apply a filterstep from vcfutils.
 \medskip
 
 Feel free to have a look at the vcf file to see how this reports the variants.
+(Use ``less course.vcf'')
 \medskip
 
 % Annotation
@@ -461,5 +465,8 @@ a try to see the effect on the output you get.
 
 % End of practical
 This is the end of the practical. We hope you now got and idea what it takes to
-work with a Linux terminal and NGS tools. Thanks for participating! 
+work with a Linux terminal and NGS tools.
+\medskip
+
+ Thank you for participating! 
 \end{document}