Parameters removed from Genrich and description of remaining parameters

exercises.md

@@ -96,24 +96,34 @@
     wget https://zenodo.org/record/3270536/files/SRR891268_R1.fastq.gz
     wget https://zenodo.org/record/3270536/files/SRR891268_R2.fastq.gz
     wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr22.fa.gz
-
-
     
-    # Build the bowtie index of the reference for the mapping
-    bowtie2-build chr22.fa.gz hg38_chr22
     
-    # Mapping
-    bowtie2 -x hg38_chr22 -1 SRR891268_R1.fastq.gz -2 SRR891268_R2.fastq.gz \
-        -I 0 -X 500 --fr --dovetail --very-sensitive | \
+    # Alignment
+    
+    bowtie2-build chr22.fa.gz hg38_chr22
+    bowtie2 -x hg38_chr22 -1 SRR891268_R1.fastq.gz -2 SRR891268_R2.fastq.gz | \
         samtools sort -n - > SRR891268.bam
-
+    
     # Peak Calling
+    mkdir
+    
     Genrich -t SRR891268.bam -o SRR891268.narrowPeak \
-        -e "chrM" -f SRR891268.log -m 0 -j -d 100\
-        -q 0.05 -a 20 -l 0 -g 100 -v \
+        -e "chrM" -f SRR891268.log -m 30 -j\
+        -a 20 -r \
         -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.
+`-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.\
+`-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.\
+`-a` is the minimum AUC for a peak\
+`-r` removes PCR duplicates.\
+`-k` creates a bedgraph-ish file for pileups. \
+
+*
     * Write the script into a Snakefile.
     * The peak caller `Genrich` is available from the `bioconda` conda channel