shift direction in ATAC/DNase data?
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6.1 years ago
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I have two set of data about ATAC-seq and DNase-seq and I like to perform peak calling using MACS2, but I found that there are some differences in shift size (plus or minus direction). I like to know which one is better for either ATAC-seq or DNase-seq (e.g. --nomodel --shift -100 --extsize 200 or --nomodel --shift 100 --extsize 200). is it right that because most accessible regions in ATAC-seq and DNase-seq located in 5' region so using --shift -100 is recommended?

ChIP-Seq MACS2 ATAC-seq DNase-seq • 1.9k views
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