I have ATAC-seq samples from which I called peaks using MACS2 to create a consensus peak file as advised by this paper. Now I would like to run nucleoatac to identify nucleosome positions.

My command:

nucleoatac run --bed consensus.broadPeaks --bam sample1.bam --fasta mm10.fa --out sample1 --cores 32";

nucleoatac run --bed consensus.broadPeaks --bam sample2.bam --fasta mm10.fa --out sample1 --cores 32";

nucleoatac run --bed consensus.broadPeaks --bam sample3.bam --fasta mm10.fa --out sample1 --cores 32";

... and so on for 32 samples.

Can I pass the same (consensus) peak file to each sample bam file?

Thank you