Question: RSAT gives strange motif calls
gravatar for rbronste
5 days ago by
rbronste160 wrote:

Hi, taking some differential ChIP-seq peaks and searching for motifs via RSAT default settings and getting some strange results. For instance as Jaspar Core Vertebrates match to the first de novo motif found in my data it gives 4 different transcription factors as matching, from 4 different families (e.g. Mef2c, Foxd3 etc.) so not sure why its not giving other members of the same family since Im assuming they would be closer. In addition across many unrelated differential peak sets I scan I get the same top motif hits which sort of appear like repeats at least on the face of it. Im wounding what may be going on here, and if I should be repeat making my ChIP-seq differential peaks before running motif analysis etc? Thanks!

chip-seq rsat motif • 69 views
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