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Step_3/Step3_Merge_Peaks_WithinRegion.sh.txt

+#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
+