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 +