Motif finding HOMER results
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11 weeks ago

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!

interpretation finding HOMER motif • 136 views
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