Spellcheck practical 2

practical_two/practical_two.tex

@@ -18,7 +18,7 @@
 }
 
 \title{NGS Introduction Course\\
-  {\Large Practical two, Piplines}}
+  {\Large Practical two, Pipelines}}
 \date{Friday, 4 April 2014}
 \author{Jeroen Laros, Michiel van Galen}
 
@@ -36,10 +36,10 @@ Log in to the virtual machine as described in the first practical. Finish these
 exercises first then continue with this one.
 \bigskip
 
-Anlysis pipelines can vary from a couple of very simple lines of code, to
+Analysis pipelines can vary from a couple of very simple lines of code, to
 complex frameworks working on multiple computing nodes. However, the idea
 behind it is always the same. Make your analysis easier, while at the same time
-it becomes reproducable, documented and easier to share.
+it becomes reproducible, documented and easier to share.
 \medskip
 
 Today we will use bash to create a basic pipeline. Unknowingly, you have
@@ -59,12 +59,12 @@ specify the interpreter. In Linux we us chmod for this.
 \medskip
 
 One last additional piece of information your system is missing, is which
-interpertaor it should use. We store this in the very first line of the script
+interpreter it should use. We store this in the very first line of the script
 and is written like this ``\#!/bin/bash''.
 \medskip
 
 This is all you need to know to write your first pipeline. Bash offers a lot
-more possibilities than just using Linux powertools, navigation and starting
+more possibilities than just using Linux power tools, navigation and starting
 other software. For example, to make the pipeline easier to re-use with other
 data, we can give a bash script parameters. Just like Bowtie, where you can
 supply your fastq file. This is done by using the reserved variable \$1 inside
@@ -99,7 +99,7 @@ a script that combines the tools from the first practical into a pipeline:
 \medskip
 
 \begin{itemize}
-  \item Inlcude these steps:
+  \item Include these steps:
   \begin{itemize}
     \item Align a fastq file to the mtDNA
     \item Convert the SAM to a sorted BAM