I have recently generated a list of motifs of TF binding sites within peaks of my ChIPseq experiment. However this list tell me how many times the motif is present within my BED file, not where, i.e. which peaks have the motif associated with them.
I could take all of the sequences of interest in the BED file and run them through JASPAR for example but this seems like a very biased way of doing it.
Is it possible in Galaxy to search within a BEDfile for a specific motif which outputs in which BEDpeak the motif was found?
If not is there any other way of doing this?
Thanks in advance to anyone who can help me.