I'm trying to answer a question I have from a manipulation study that unregulated DEGs (from a standard RNA-seq) contain an enrichment of the N6-methyladenosine consensus motif (DRACH), and therefore the assumption being these transcripts are bound more often by associated m6A proteins (which we have a CLIP-seq coming to show).

To do this, I used homer on a gene-set of up-regulated DEGs that I calculated using edgeR, however when I set the parameters to -rna (see: http://homer.ucsd.edu/homer/motif/rnaMotifs.html) I get only miRNA hits, despite seemingly to have a DRACH motif as the top enriched motif (see image attached).

My question is, should I use my own custom motif file for this instead? Or is there another way to do this that I'm missing.

Homer command:

findMotifs.pl upregulatedDEGs_refseq.txt rat MotifOut/ -rna -len 8