To add to my post, I reread the macs documentation and it seems that the fdr is calculated based on the p value of negative peaks, regardless of their location. That is to say, a strong peak on one chromosome could be associated with a high fdr bc of an even stronger negative peak, anywhere in the genome. So, is the fdr then the percent of negative peaks relative to total peaks (pos + neg) at or below a certain p value ?
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