histone_centered_processing.sh

# Processing Histone centric data

bedops --everything  H3K4me1_filtered_peaks.bed H3K27ac_filtered_peaks.bed | bedops -m --range -1 - > Histone_putative_enhancers.bed

# RPKM Filtering
# Get RPKM
./rpkm.py --peaks Histone_putative_enhancers.bed --experiments h3k4me1_list.csv -f H3K4me1_hc
./rpkm.py --peaks Histone_putative_enhancers.bed --experiments h3k27ac_list.csv -f H3K27ac_hc