Q: question about peak name

[bioysu]

Use case I tried to analyze ATAC-seq data with MACS2 as following: macs2 callpeak -t input.bed -f BED -n sampleName -g mm -p 0.1 --nomodel --shift 100 --extsize 200 -B --SPMR --call-summits --outdir /output Describe the problem I am confused with the peak names in the output files: 1 3495637 3496463 sampleName_peak_3a 28 . 2.20978 2.89339 1.32929 117 1 3495637 3496463 sampleName_peak_3b 48 . 2.84115 4.89429 3.20113 456 There are two peaks for sampleName_peak_3, sampleName_peak_3a and sampleName_peak_3b, which one I should use in following steps?

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[taoliu]

@bioysu When -call-summits is used, MACS2 will call the subsummits in the peak region, and that's why you see sampleName_peak_3a and sampleName_peak_3b. It means there are two local maxima in the peak region 1 3495637 3496463. To choose which one in the downstream analysis, depends on your purpose. If you want to look for motifs at the 'most accessible' regions in the peak, you may take both positions into account -- check the _summit.bed output for the coordination of the subsummits.