#!/bin/sh
#$ -cwd

module load EBModules pybedtools/0.9.0-GCC-11.3.0
bedtools intersect -wa -u -a T1P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T2P_P2F3_hg38_callpeaks_peaks.narrowPeak > PT1vPT2_POU2F3.bed 
bedtools intersect -v -a T1P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T2P_P2F3_hg38_callpeaks_peaks.narrowPeak > PT1vPT2_POU2F3_a_only.bed 

bedtools intersect -wa -u -a T1P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T1P_HA_hg38_callpeaks_peaks.narrowPeak > T1P_P2F3vsHA.bed 
bedtools intersect -v -a T1P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T1P_HA_hg38_callpeaks_peaks.narrowPeak > T1P_P2F3vsHA_a_only.bed 

bedtools intersect -wa -u -a T2P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T2P_HA_hg38_callpeaks_peaks.narrowPeak > T2P_P2F3vsHA.bed 
bedtools intersect -v -a T2P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T2P_HA_hg38_callpeaks_peaks.narrowPeak > T2P_P2F3vsHA_a_only.bed 

bedtools intersect -wa -u -a P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T1P_P2F3_hg38_callpeaks_peaks.narrowPeak > PvsT1_P2F3.bed 
bedtools intersect -wa -u -a P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T2P_P2F3_hg38_callpeaks_peaks.narrowPeak > PvsT2_P2F3.bed
bedtools intersect -v -a P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T1P_P2F3_hg38_callpeaks_peaks.narrowPeak > PvsT1_P2F3_a_only.bed
bedtools intersect -v -a P_P2F3_hg38_callpeaks_peaks.narrowPeak -b T2P_P2F3_hg38_callpeaks_peaks.narrowPeak > PvsT2_P2F3_a_only.bed