For ATAC-seq, they represent likely TF binding sites. Smoothed signal summits show strong PhastCon scores. Raw signal summits show flanking enrichment of PhastCon scores. The raw signal summits are (imo) one of the "shoulders" of TF footprints, in ATAC anyway
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Thank you both, your comments are highly appreciated!
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Yes summits are certainly relevant for TF ChIP-seq/exo/nexus like experiments as well as DNase-seq/ATAC-seq. Peak callers have variable precision at calling one (or more) summits per peak. Summits are only approximate estimates of primary binding site. Use sequence to home in.
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in contrast, summits for histone ChIP-seq are primarily marking approx. location of marked nucleosomes. So shud be interpreted accordingly. Also much more fuzzy.
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