Question: API for searching for adjacent genes
0
gravatar for VictoriaP
11 months ago by
VictoriaP10
South Africa/Cape Town/UCT
VictoriaP10 wrote:

Hi, is anyone able to advise whether there is an API available to find adjacent upstream or downstream genes from a given gene location?

I am looking at viral insertions in the human genome, and once I've identified the viral insertion points, I need to identify what genes are in the flanking regions.

Any advice is appreciated. Thank you

ADD COMMENTlink modified 11 months ago by WouterDeCoster44k • written 11 months ago by VictoriaP10
1
gravatar for WouterDeCoster
11 months ago by
Belgium
WouterDeCoster44k wrote:

I would get a bed file of human genes and use bedtools closest

ADD COMMENTlink written 11 months ago by WouterDeCoster44k

Do you know how to create a BED file from a VCF file? - I have multiple vcf files with viral insertion data, that I need to use to make a BED file to then use with bedtools as you previously suggested.

ADD REPLYlink written 4 months ago by VictoriaP10
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