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genes close to random genomic locations

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
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written by sumithrasank75 sumithrasank75

Try the UCSC Genome Browser's mysql databases?

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written by Ram Ram

1 answer

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

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updated by Alex Reynolds Alex Reynolds • written by GenoMax GenoMax

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?

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written by sumithrasank75 sumithrasank75

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