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7.6 years ago
BioinfGuru
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2.1k
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