Question: Identifying individual sequences which have specific motifs
gravatar for alice.roworth
5.7 years ago by
United Kingdom
alice.roworth10 wrote:


I have a large dataset from a ChIP-seq experiment. I am trying to identify different co-factors which may bind differently across different treatments. To do this I have uploaded my peaks into CentDist which outputs motifs enriched across all peaks and I have identified a handful which are unique to one treatment.

To validate these hits, I'm going to need to identify which specific peaks have these motifs. For example if I have 10 peaks (named 1-10) and I find that NFKB motifs are ranked highly in this set, I need to find which peaks (e.g. 2-5, 7,9) this corresponds to.

I can in theory get this information from TRANSFAC, but I have to download data for all motifs (not just the ones I am interested in) at each peak separately and with over 2500 peaks I am not super keen on doing this.

Does anyone know of a tool I can use to pull this information out? Ideally this will be something simple to use as I am no coder / bioinformatics expert!


transfac chip-seq centdist • 1.3k views
ADD COMMENTlink written 5.7 years ago by alice.roworth10
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