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Do you already have the co-ordinates of the defined promoters?; or are you just saying that, generally, you are assuming that they are +/- 2kb from the TSS?
I am just generally trying to cover a large enough area to exclude most promoter elements, maybe +/-2.5kb is even more appropriate.
Any other ideas? Thanks!
You could download a reference template of genes and promoter regions from the UCSC Table Browser in BED format, and then use
bedtools intersect, or something like that, in order to overlap your current regions to the actual defined promoters.How can I fetch promoter sequence upstream of a gene?
Kevin