changed description regarding paired-end mode, removed mkdir, instructions to...

changed description regarding paired-end mode, removed mkdir, instructions to create an new directory

exercises.md

@@ -105,7 +105,6 @@
         samtools sort -n - > SRR891268.bam
     
     # Peak Calling
-    mkdir
     
     Genrich -t SRR891268.bam -o SRR891268.narrowPeak \
         -e "chrM" -f SRR891268.log -m 30 -j\
@@ -113,9 +112,9 @@
         -k SRR891268.bg
     ```
 
-* Atac-seq is similar to ChIP-seq an epigenomics NGS technique to identify open chromatin. Since the sequencing is in a paired-end mode (instead of single-end like ChIP-seq) other parameters are needed for the alignment.
+* Atac-seq is similar to ChIP-seq an epigenomics NGS technique to identify open chromatin. Since the sequencing is in a paired-end mode (instead of single-end like we had in the previous data set from the tutorial) other parameters are needed for the alignment with `bowtie2`.
 `-1` indicates the forward read while `-2` indicates the reverse read.\
-`Genrich` has an advantage over `MACS2` since it is offering to do necessary filtering steps during the peak calling.\
+`Genrich` has an advantage over `MACS2` since it is offering to do the necessary filtering steps during peak calling.\
 `-e` allows to exclude chromosomes that are specified. In this case the mitochondrial chromosome (chrM). \
 `-m` filters low quality reads. \
 `-j` specifies that it has to run in the atac-seq mode.\
@@ -125,6 +124,12 @@
 
 *
     * Write the script into a Snakefile.
+        * Create a new directory `atac-seq` in your home directory for this (see the code below)
+        ```bash
+        $ cd
+        $ mkdir atac-seq
+        $ cd atac-seq
+        ```
     * The peak caller `Genrich` is available from the `bioconda` conda channel  
     
 2. How can you improve the workflow in the context of data management? Think about data structures and log files.