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to MEME Suite Q&A
Hmm. You've set the -meme-minw and -meme-maxw options appropriately. Are the motifs identified by MEME or by DREME?
Could you attach the messages.txt file from the MEME-ChIP output directory and the meme.html file from the meme_out directory under the MEME-ChIP output directory? That would help us troubleshoot the problem.