I am trying to download all the human ATAC-seq peak from ENCODE. They have a page to allow you filter the samples, and generate a url file contains urls of the selected samples.
My main question is on the "Available file types" section. They allow to select bed narrowPeak and bed idr_ranked_peak. If bed narrowPeak is selected, the "File format type" tab in the generated meta files will contain the following files: conservative IDR thresholded peaks, IDR thresholded peaks, pseudo-replicated peaks, replicated peaks . Each would be one bed file. If bed idr_ranked_peak is selected, the "File format type" tab in the generated meta files will only contain idr_ranked_peak.
From the name, I feel conservative IDR thresholded peaks, IDR thresholded peaks, and idr_ranked_peak are IDR filtered for peak concordance among replicates. But how are they different?
