I'm using homer on a bunch of regions that have been called as having peaks to do motif discovery. Homer (http://biowhat.ucsd.edu/homer/ngs/peakMotifs.html) docs say that it needs a strand parameter. Since the regions are from a ngs experiment where the library sequenced is unstranded, the strand has no meaning and my peaks are unstranded. In that case, what's the correct way to feed the regions to Homer? If I give it a BED with no strand value in the 4th column, it appears to run but I have no idea how it handles this case. Will the
-rna parameter make it ignore strand? Ultimately I want it to avoid strandedness when determining the motif.
I think that MEME can be made to ignore strand but not sure about Homer.