Q: HMMRATAC cutoff analysis need help with choosing cutoffs

[budeer]

Hi,
Thank you so much for developing the MACS3 HMMRATAC program!
My ATAC-Seq data is from mouse ES cells. After running the cutoff analysis, I'm trying to use the fold change score to determine appropriate lower, upper and pre-scanning cutoffs. As shown in the cutoff analysis document attached, at the score 99, we're already at 3864 peaks, and if the lower cutoff is ~10k peaks according to the documentation, the lower cutoff should be ~60? I am not sure what our upper cutoff should be, according to the documentation, "The upper cutoff should be the cutoff in the cutoff analysis result that can capture some (typically hundreds of) extremely high enrichment and unusually wide peaks.", but as seen in my data set, there are >3000 extremely high enrichment peaks, but they're not "Unusually wide", in fact, those high score peaks are only about ~300 bp on average. I'm not sure what to do here. Should I keep these high scoring peaks, and set -u to be 100, -l to be 60? I am also not sure where the -c should be. Please advice. Thank you so much for your help!
Cutoff analysis flox-ETOH.txt