getPromoters

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guoyou88 • 0

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Last seen 3.1 years ago

United States

How does getPromoter( ) function in ChIPseeker retrieve one promoter for each gene and not consider other alternative promoters of different transcripts?

Thanks!

ChIPseeker • 1.3k views

ADD COMMENT • link 3.1 years ago guoyou88 • 0

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My intuition is that it returns the "TSS" of the genes table (instead of looking at the transcripts table), that is to say the start of + genes or the end of minus genes. Usually the genes coordinates are inclusive, they include the entire range of all the transcripts, so the gene's TSS would be the most upstream (+ genes) or the most downstream (- genes) transcript TSS.

ADD REPLY • link 3.1 years ago Guillaume Devailly ▴ 60

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Thanks for your reply. It's very likely the getPromoter function works as you said. When I perform intersection between ChIPseq peaks and promoters, the promoters affect the result. I think it's better to obtain promoters for all transcripts.

Thanks!

ADD REPLY • link 3.1 years ago guoyou88 • 0

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