#!/bin/bash
#$ -cwd -V

module load EBModules deepTools/3.5.2-foss-2022a

bamCompare -b1 P_P2F3_hg38_sorted.bam -b2 P_IgG_hg38_sorted.bam -o P_P2F3_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads

bamCompare -b1 P_HA_hg38_sorted.bam -b2 P_IgG_hg38_sorted.bam -o P_HA_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads

bamCompare -b1 T1P_P2F3_hg38_sorted.bam -b2 T1P_IgG_hg38_sorted.bam -o T1P_P2F3_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads

bamCompare -b1 T1P_HA_hg38_sorted.bam -b2 T1P_IgG_hg38_sorted.bam -o T1P_HA_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads
bamCompare -b1 T2P_P2F3_hg38_sorted.bam -b2 T2P_IgG_hg38_sorted.bam -o T2P_P2F3_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads
bamCompare -b1 T2P_HA_hg38_sorted.bam -b2 T2P_IgG_hg38_sorted.bam -o T2P_HA_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads


bamCompare -b1 P_H3K27ac_hg38_sorted.bam -b2 P_IgG_hg38_sorted.bam -o P_H3K27ac_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads
bamCompare -b1 T1P_H3K27ac_hg38_sorted.bam -b2 T1P_IgG_hg38_sorted.bam -o T1P_H3K27ac_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads
bamCompare -b1 T2P_ H3K27ac_hg38_sorted.bam -b2 T2P_IgG_hg38_sorted.bam -o T2P_ H3K27ac_hg38_sorted.bw --binSize 20 --effectiveGenomeSize 2913022398 --blackListFileName /grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklist.bed --smoothLength 60 --centerReads