Question: Splitting .bed file by genomic location
gravatar for rbronste
18 days ago by
rbronste150 wrote:

Hi, pretty simple question - wondering about the easiest way to take a single .bed file and split the ranges into those at defined mm10 promoters and those that are intergenic/intronic. With the promoter being +/- 2kb from the TSS? Thanks!

bed chip-seq promoter R • 128 views
ADD COMMENTlink modified 18 days ago • written 18 days ago by rbronste150

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?

ADD REPLYlink written 17 days ago by Kevin Blighe11k

I am just generally trying to cover a large enough area to exclude most promoter elements, maybe +/-2.5kb is even more appropriate.

ADD REPLYlink written 16 days ago by rbronste150

Any other ideas? Thanks!

ADD REPLYlink written 12 days ago by rbronste150

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?


ADD REPLYlink written 12 days ago by Kevin Blighe11k
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