Super-enhacer identification with ATAC-Seq
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ROSE expects H3K27ac data, not open chromatin signals. Whatever result you'll get is not what the tool has been designed for.
I see, in other words, ATAC-seq data doesn't correlate well with H3K27ac
No, most H3K27ac regions should be in ATAC-seq (open chromatin) domains, but not vice versa.