Spacer length analysis using MEME
Hi, I am new to ChIP-Seq analysis and want to get a spacer length distribution in my TF binding peaks using MEME. I used MEME-ChIP for motif enrichment and my TF binding site was enriched with a significant E-value, 1.3e-091. My half-site was not too significantly enriched with DREME E=1.2e-002 and the SpaMo analysis did not reveal anything when I used the enriched MEME motif as the "primary motif sequence". I was wondering if there was a standard procedure to follow for motif spacer analysis using MEME. Is SpaMO a good program to use for this purpose? Please let me know, thank you.
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