I notice when using tools like HOMER there are two different types of outputs: de novo motifs vs known motifs and it seems no matter what the data is (type of ChIP etc.) there is always a "de novo" motif set in the results.
I was hoping to reach out to experts on insight about how much of the space of motif based structure, within a genome, has been identified. Is there any consensus on what portion of the motif like patterns, for example in human or mouse genome, have been identified? When I find de novo motifs using HOMER in my ChIP-seq or ATAC peaks, what are the chances that in my common-place ChIP experiment (PU.1 for example) I find de novo motifs, not recorded in the databases (i.e. JASPER).