intervene_figure.sh

# Make overlap of enhancer data


cp ../H3K4me1_filtered_peaks.bed H3K4me1_enhancers.bed
cp ../H3K27ac_filtered_peaks.bed H3K27ac_enhancers.bed
cp  ../SUNP_filtered_peaks.bed .
cp  ../SSP_filtered_peaks_merged.bed .
cut -f1,2,3,4  ../SUNP_filtered_peaks.bed > t
cut -f1,2,3,4 ../SSP_filtered_peaks_merged.bed >> t
sort-bed t | uniq > GRO-seq_enhancers.bed
cp ../Histone_pe_filtered_peaks.bed Histone_enhancers.bed

intervene upset -i H3K4me1_enhancers.bed Histone_enhancers.bed GRO-seq_enhancers.bed --filename --order degree  --sxlabel "No. of Unique Enhancers" --dpi 1200  --figsize 10 8 --mbcolor "#108DCC"  --sbcolor "#E62128"

# All called example:
chr18:46,445,713-46,491,500

# Only Histone example:s
chr13:28,478,659-28,505,753
chr17:40,680,519-40,696,946
chr1:163,032,837-163,048,183

# Only GRO-seq:
chr6:106,622,704-106,798,241
chr16:9,750,783-9,780,659