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

intervene upset -i *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:
chr3:38,959,553-39,174,357
chr13:28,478,659-28,505,753

# Only GRO-seq:
chr6:106,622,704-106,798,241