Question: genes close to random genomic locations
gravatar for sumithrasank75
3.8 years ago by
United States
sumithrasank75140 wrote:

I would like to pick a 1000 random locations in the human genome (say hg19 assembly) and get a list of the genes closest to them. Can you suggest how I can go about this?

gene • 788 views
ADD COMMENTlink written 3.8 years ago by sumithrasank75140

Try the UCSC Genome Browser's mysql databases?

ADD REPLYlink written 3.8 years ago by RamRS30k
gravatar for genomax
3.8 years ago by
United States
genomax92k wrote:

Generate your random intervals from hg19 assembly using bedtools random (documentation) and then use bedtools closest (documentation).

A solution using closest-features in the BEDOPS toolkit: N Closest Genes To A Given Location

ADD COMMENTlink modified 3.8 years ago by Alex Reynolds31k • written 3.8 years ago by genomax92k

I read through the bedtools random documentation. It uses a file hg19.genome. Is this file in bed format and how can I download it?

ADD REPLYlink written 3.7 years ago by sumithrasank75140

You can find hg19.genome file here. It is a file with lengths of chromosomes.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by genomax92k
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