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 0000000000000000000000000000000000000000..14b8d773fb4ca44d7939ac6c36f442b267fc8d94
--- /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
+