# Make universe of Peak regions
bedops --everything /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/ES_D10/call-transcripts.sh-1.0.0/final-transcripts.bed \
    /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/ES_D2/call-transcripts.sh-1.0.0/final-transcripts.bed \
    /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/ES_D0/call-transcripts.sh-1.0.0/final-transcripts.bed \
    /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/ES_D7/call-transcripts.sh-1.0.0/final-transcripts.bed \
    /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/ES_D5/call-transcripts.sh-1.0.0/final-transcripts.bed \
    >  /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/universe_transcripts/merge_final-transcripts.bed


# Seperate into +/- strand
awk '$6 == "+"' /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/universe_transcripts/merge_final-transcripts.bed > /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/universe_transcripts/merge_final-transcripts.pos.bed
awk '$6 == "-"' /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/universe_transcripts/merge_final-transcripts.bed > /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/universe_transcripts/merge_final-transcripts.neg.bed


# Find overlapping fraction by at least 80%
bedmap --echo-map --fraction-both 0.8 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/GRO-seq/universe_transcripts/merge_final-transcripts.pos.bed \
    | awk '(split($0, a, ";") > 1)' - \
    | sed 's/\;/\n/g' - \
    | sort-bed - \
    | uniq - \
    | head