When executing HOMER for motif discovery (with options -fasta -noreopp -noknown), 2 of the main files it outputs are
homerMotifs.all.motifs describing the results. I was expecting the results described in these 2 files to be identical, but the file
homerMotifs.all.motifs often has more motifs than the html file. I cannot figure out if it's because a threshold is used and the html is a "filtered" file. Some motifs that are present in the
all.motifs file are absent from the html file despite having better p-value and %of target ratio then others that are kept and shown. What explains this difference?