
# Get All GRO-seq enhancers
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

# Histone Processing

./rpkm.py --peaks GRO-seq_enhancers.bed --experiments h3k27ac_list.csv -f H3K27ac --minimum 0
./rpkm.py --peaks GRO-seq_enhancers.bed --experiments h3k4me1_list.csv -f H3K4me1 --minimum 0
./rpkm.py --peaks GRO-seq_enhancers.bed --experiments input_list.csv -f Input --minimum 0


#GRO-seq Processing
grep name SSP_filtered_peaks_sum.tsv | cut -f2,3,4,5,6,7 > GRO_filtered_peaks.tsv
cut -f2,3,4,5,6,7 SSP_filtered_peaks_sum.tsv | grep -v name >> GRO_filtered_peaks.tsv
cut  -f4,7,8,9,10,11 SUNP_filtered_peaks.tsv | grep -v name >> GRO_filtered_peaks.tsv


# RNA-seq
