Hey all,
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,
Nick
The bindingSites option can accept an GRanges object with binding score by any tools that can predict the binding sites. Please note that the "score" must be a column in the metadata. That means you can use matchPWM or fimo to predict the binding sites.
The output of factorFootprints is very similar to centipede and DNAPOS. I add Profile.segmentation with distalabun and proximalabun to present the distal abundance and proximal abundance (which is show as red dash line in the figure). The abundance are calculated by average the signal from the center of binding sites to the end of distal sites you defined, and then use optimal segmentation approach to split then into proximal and distal. The binding is the site motif binding. For more information, you can refer: Epigenome characterization at single base-pair resolution and Genome-wide footprinting: ready for prime time?.
Hope this help.
Jianhong.