# 31676868 HiSeq2500 Bowtie2 v2.3.4.1 default Remove reads mapped to ENCODE blacklist Remove reads mapped to noncanonical chromosomes Remove reads mapped to mitochondrial DNA Remove duplicates using samtools v1.8 markdup Aligned reads from replicates were merged into a single BAM file to identify a comprehensive set of peak. Next, use the comprehensive peak set to compute read counts separately for each replicate and condition. The generated matrices were normalized and analysed by DESeq2. MACS2 v2.1 callpeak # ATAC -q 0.05 -nomodel -shift -100 -extsize 200 # ChIP/H3K27Ac -broad -broad-cutoff 0.1 --nomodel HOMER v4.8.2 / findMotifGenome.pl -size given -bits -mask Only enriched sequences present in > 1.5% matchs were retained #31839570 # ChIP Histone mark bowtie2 default MACS2 -broad-qvalue 0.01 whole-cell extract as the background control # ATAC bowtie2 default MACS2 --nomodel -shift 37 -extsize 73 # half nucleosome -broad -qvalue 0.01