promoters hg38 coordinates

Question

[Morris_Chair]

Hello everyone, Do you know if there is any easy way to get human genes promoters coordinates?

like a link from where I can download it

thanks

Answer 1

[jared.andrews07]

ChIPseeker has a function for this.

[Morris_Chair]

Hello Jared, thank you for the answer

I used ChIPseeker but unlesss I'm doing something wrong it doesn't includes the coordinates of a promoter but only how far it is the peak from it. I know it includes also the start and the end of the genes but then, is it included in this range the promoter as well ?

I think would be good to have a list of promoters coordinates and filter out genes from my peaks.bed file

Thank you

[jared.andrews07]

I see. Something like this should work then:

library("TxDb.Hsapiens.UCSC.hg38.refGene")
tx <- TxDb.Hsapiens.UCSC.hg38.refGene
proms <- promoters(tx)

See ?promoters for changing the upstream/downstream lengths.