Question: extract genes and functions +/-50kb around a SNP
0
gravatar for sonia.olaechea
15 months ago by
sonia.olaechea130 wrote:

Hi everyone,

I have a list of SNPs (rs) and I would like to extract all the genes and their functions that are located 50kb up- and downstream of them. I've been trying to generate the links to the corresponding pages of UCSC with Excel (which is more or less automatized). But I would like to find a way to directly obtain a file (.txtor .csv) with the information I need. Can anyone recommend a more automatized method with e.g an R package to obtain this information? Thank you very much in advanced!

snp gwas • 370 views
ADD COMMENTlink written 15 months ago by sonia.olaechea130
1

duplicate How To Map A Snp To A Gene Around +/- 60Kb ?

ADD REPLYlink written 15 months ago by Pierre Lindenbaum130k

Hi Pierre, I'm trying to use the mysql solution you proposed in your other post, but mysql gives me the following error: ERROR 1146 (42S02) at line 2: Table 'hg19.snp130' doesn't exist. Is this because I'm looking at a deprecated table? Is there maybe a more updated one for snp information? Thanks in advance!

ADD REPLYlink modified 15 months ago • written 15 months ago by sonia.olaechea130
2

Try snp151 which is the current one and be sure to have the corret genome version hg19 <=> hg38.

ADD REPLYlink modified 15 months ago • written 15 months ago by ATpoint38k

Great, working! But... where can I find the list of tables from which to choose the information?

ADD REPLYlink written 15 months ago by sonia.olaechea130

which information?

ADD REPLYlink written 15 months ago by ATpoint38k

I'd like to find the names of the genes that are 50kb up- and downstream of my list of rs and also their functions, pathways in which they are involved and their disease associations.

ADD REPLYlink written 15 months ago by sonia.olaechea130

Hi Pierre, Would you please update your answer to reflect the current dbSNP version?

ADD REPLYlink written 8 months ago by reza.jabal420
1

Get coordinates or the rs in BED format ( Get Rs Number Based On Chromosome and Position ), then define a 50kb window around these using BEDtools slop and then use BEDtools intersect to intersect these windows with a GTF annotation file to get the respective genes.

ADD REPLYlink modified 15 months ago • written 15 months ago by ATpoint38k
1

Hi, well if you only want genes, then I would suggest downloading complete gff or similar format for your organism, and then do simple selection of rows within desired range. In good gff, there is already some functional annotation present, but with accession number for the gene you certainly will be able to look into your favourite database. Best regards

ADD REPLYlink written 15 months ago by massa.kassa.sc3na270

'with Excel'

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ADD REPLYlink written 15 months ago by Pierre Lindenbaum130k
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