From 4b8e0f3497c29ee13ce1e96867190ba7e21b3f2f Mon Sep 17 00:00:00 2001
From: Robert Phillips <rphill3@uab.edu>
Date: Mon, 29 Jun 2020 18:13:40 -0500
Subject: [PATCH] Upload New File

---
 Step_3/Step3_Merge_Peaks_WithinRegion.sh.txt | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 Step_3/Step3_Merge_Peaks_WithinRegion.sh.txt

diff --git a/Step_3/Step3_Merge_Peaks_WithinRegion.sh.txt b/Step_3/Step3_Merge_Peaks_WithinRegion.sh.txt
new file mode 100644
index 0000000..14b8d77
--- /dev/null
+++ b/Step_3/Step3_Merge_Peaks_WithinRegion.sh.txt
@@ -0,0 +1,13 @@
+#Load bedtools
+module load BEDTools
+
+cd /data/user/rphill3/Enhancer_Ident_ATAC/Final_PeakCalls
+
+for i in *.narrowPeak.bed
+do
+#sort the bed
+sort -k1,1 -k2,2n $i > Sorted_beds/$i.sorted.bed
+#merge peaks within 1000bps of each other 
+bedtools merge -i Sorted_beds/$i.sorted.bed -d 1000 > Merged_beds/$i.sorted.merged.bed
+done
+
-- 
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