From 959f34d18c01f0d8b04cec2de64fae4df41d2f1e Mon Sep 17 00:00:00 2001
From: nicolas-zimmermann <nicolaszimmermann.snv@gmail.com>
Date: Thu, 24 Oct 2019 14:33:06 +0200
Subject: [PATCH] added script for question 1 and question 2

---
 wgs.sh | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/wgs.sh b/wgs.sh
index a9bf588..177fa76 100644
--- a/wgs.sh
+++ b/wgs.sh
@@ -1 +1,26 @@
 #!/bin/bash
+
+mkdir results
+
+# Question 1
+soft/bowtie2 --end-to-end --fast -x databases/all_genome.fasta -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -S results/alignment.sam
+
+# Question 2
+
+# a
+samtools view -b results/alignment.sam
+
+# b
+samtools sort -@ 4 results/alignment.bam -o results/alignment.sorted.bam
+
+# c
+samtools index results/alignment.sorted.bam
+
+# d
+samtools idxstats -@ 4 results/alignment.sorted.bam > results/alignment.idx
+
+# f
+grep ">" databases/all_genome.fasta|cut -f 2 -d ">" > results/association.tsv
+
+# Question 3
+