Set up environment and copy over files
module load StdEnv/2020 samtools/1.11 r/4.0.2
export PATH="/home/hgen_share/Anaconda/bin:$PATH"
export PATH="/home/hgen_share/Anaconda/envs/chip_seq_V2/bin:$PATH"Produce coverage track with bamCoverage
bamCoverage -b KO_H3K27ac.chr1.bam -o KO_H3K27ac.chr1.bwAggregate signal around promoter regions using computeMatrix
computeMatrix reference-point -R promoter.chr1.bed -S KO_H3K27ac.chr1.bw -o KO_H3K27ac.promoter.chr1.mat.gz --referencePoint center -bs 100 -a 10000 -b 10000Visualize output through plotHeatmap
plotHeatmap -m KO_H3K27ac.promoter.chr1.mat.gz -o KO_H3K27ac.promoter.chr1.pdf --legendLocation none --yAxisLabel "" --xAxisLabel "" --colorMap magma --regionsLabel "" --refPointLabel "Promoter"Download .bw and .pdf result files to your local computer
Identify significantly enriched regions using macs3
macs3 callpeak -t KO_H3K27ac.chr1.bam -c KO_Input.chr1.bam -f BAM -g 2.4e8 -n KO_H3K27ac.chr1 -q 0.01Download .narrowPeak file to your local computer