I am running HOMER to find known motif enrichment on differentially methylated regions (DMR). The target consists of fasta sequences corresponding to DMR and I have also provided a background file. I can run the commands fine.
But I was wondering if I can get the intermediate output from HOMER where all potential motifs for each sequence in the fasta file is provided. Right now I can see the # Target sequences with a particular motif, but these are only the significant ones. Is there a way I can get all sequences for a motif, irrespective of being significant or not?
Thank you, Sharmi