Hi! Now I have 6 ATAC-seq samples which have been aligned to hg19 and called peaks by MACS2. 3 of them are from A cells and the other are from B cells. Now I'm going to do differential peak calling by MACS2. Before it, I need to merge peaks from 3 samples of the same cell type. I use this command to call peaks.
macs2 callpeak -B -t sample_1.bam -n sample_1 --nomodel --extsize 120 --shift 60 \ --outdir sample_1 --keep-dup all
And then I get 5 output files.
sample_1_control_lambda.bdg sample_1_peaks.narrowPeak sample_1_peaks.xls sample_1_summits.bed sample_1_treat_pileup.bdg
But I'm confused how to merge them. Shall I use bedtools intersect to merge 3 control_lambda.bdg files and treat_pileup.bdg files of A cell respectively? I'm worried if it will influence the value in the fourth column of the bdg files.
Or shall I merge their bam files before peak calling?