Question: genes close to random genomic locations
0
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
3
gravatar for genomax
3.8 years ago by
genomax92k
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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