Hello, I have a question regarding an output from the HOMER motif finding software.
I have used "annotatePeaks.pl tss" to find a custom motif that I have generated with "seq2profile.pl" at +/- 10 kb of a list of genes of interest. When looking at the results.txt, some motif instances occur twice, once on the (+)-strand and once on the (-)-strand but with exactly the same position (in bp from the TSS) and exactly the same sequence.
I am not sure how to interpret these "duplicates", does someone have experience with this? Help would be greatly appreciated!