Question: HOMER findMotifsGenome.pl Local Optimisation Phase
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gravatar for janepuh12
14 months ago by
janepuh120
janepuh120 wrote:

Hello, I am using Homer for de novo motif discovery in ChIP-seq peaks in BED format. After a local optimization phase, I receive a message: 'Remaining seeds don't look promising (After initial 5 motifs, logp -8.403 > -9.134)' What does this message mean? Does it mean that there are less enriched motifs than 25 in my dataset? Can I consider my results reliable? All the output files look correct, the file 'homerResults' contains 18 motifs, 16 of them are possibly false positive (with p-value higher than 1e-10).

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