I’ve been using the factorFootprints() from the ATACSeqQC package. First basic question is the bindingSites option. Is this supposed to be a Granges object of the ATAC peaks to search through or a list motif binding sites identified by matchPWM()? I’ve been using matchPWM to find instances of the motif across the genome and then intersecting this list with my ATAC peaks and using the resulting intersection as the binding sites. Is this correct way to use the tool to find the motif instances in my ATAC peaks?
Relating to the same function factorFootprints – the output contains a Profile.segmentation with pos distalabun proximalabun and binding. I was just wondering how each of these categories is calculated. In addition what is the range for binding? I'm assuming the higher number the but I don’t yet have a grasp on what constitutes “binding”.
Thanks for your help,