HOMER peak-motif relationship as direct-indirect binding

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Hello,

I am conducting ChIP-seq analysis.
I have HOMER annotated motif list assigned to every peak in MACS2 result. I have an example ANNOTATED KNOWN MOTIF RESULT

(by the way I could not fit all of the information that excel files has but in the first column there are simply peak names)

I wonder, could it be interpreted as; if there is motif(like in the first line) of the subjected TF factor is directly binding, and if there is no motif found(like in the second line) there is indirect binding.

Thank you for any idea in advance!


homermotif


directbinding


indirectbinding

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