I have about 200 short nucleotide motifs (6-12 bp in length) from the human genome, and I'm trying to see how conserved they are across vertebrates.
I was thinking that I'd need to make a bed file for each motif that lists all of its occurrences in the human genome. From there, I could map the beds to a bigwig files of PhastCons scores (essentially doing the reverse of what the PhastCons software was designed to do). Does that sound like the best approach?
I'm getting stuck at the step of going from motifs to bed files. I've tried using BLAST to find all occurrences of motifs, but their short length is causing issues.
I've tried messing with the e-value threshold, word size, and filter parameters, but I still don't get any hits.
Is there a work-around for this issue, or should I just rethink my entire approach?