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  • interpretation of binding motif from a list

    interpretation of binding motif from a list
    I have a dumb question but certainly I have to admit I am lost. I am analyzing Chip-seq data and used various tools like Cisfinder/ Hommer and get a list of various motifs which have Fre, ratio score and FDR. Now my question is which one/ several criteria’s I should be using to pin point probable motif- just FDR? Rato?
    Any pointers or papers will be helpful

    Thanks

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