I'm trying to generate motif density histograms around several peak files. For each peak file the output always shows a motif frequency of 0 at every bin. I know for sure that the motif is present around these peaks because they show in the output when running annotatePeaks normally, and they are definitely within +/- 500bp of the peaks. I suspect something may be wrong with my input files, or maybe there's something else I'm missing. Unfortunately, the Homer website doesn't have much info on this section.

Here is my command:

annotatePeaks.pl HIF1A_peaks.txt hg38 -size 1000 -hist 10 -m stat3.motif > outputfile.txt

Motif file: https://pastebin.com/C5TL0PLe

Peak file: https://pastebin.com/ZwLwKFDU

Output: https://pastebin.com/0Gk7gdga The first column contains the bins, the last 4 columns are nucleotide frequencies. The 3 columns with all 0s are where motif frequencies are supposed to show.

Input and output across all peak files I'm using pretty much looks like what I've just shown.

Is there anyone who has more experience with this? Or maybe there's another tool that accomplishes the same thing.