Centrimo from the MEME-suit --neg option

Question

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Hi,

I have peaks and negative peaks (i.e. I switched the IP and input files). I ran centrimo individually on each file and got a list of motifs. Now I used the centrimo --neg option to see how they plot against each other, to assess the motifs found and I got a different looking graph than what I expected - the 'negative' motifs look different than when I ran them individually.

This is what meme says about this option:

plot motif distributions in this set as well in the <sequence file=""> (positive sequences) and compute the relative enrichment

Maybe the way the --neg option works is different from my understanding of it? I checked the meme paper without success https://academic.oup.com/nar/article/40/17/e128/2411117

This is my cmd:

centrimo --o peaks_motif_vs_neg_all --neg NEG.fasta --norc pos_fasta pos_meme/meme.txt

I'll appreciate any help :)

Answer 1

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I figured it out!

When I ran the negative peaks on their own I was looking for the motifs that are in the negative peaks When I ran the --neg option it takes the motifs that were indicated in the positive peaks and checked these positive motifs to see if they are enriched or depleted in the same areas. So, basically, these are two different questions and that's why they did not give similar results.