Question: unannotated SNP ids
0
gravatar for m_02
4.4 years ago by
m_0220
United States
m_0220 wrote:

Hi all,

I have a list of unannotated SNPs ,i want to find those genes which are present 10kb upstream and downstream of that unannotated SNP.

Thanks in advance

 

snp • 967 views
ADD COMMENTlink modified 4.4 years ago by iraun3.7k • written 4.4 years ago by m_0220
1

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

ADD REPLYlink written 4.4 years ago by Pierre Lindenbaum128k
1
gravatar for iraun
4.4 years ago by
iraun3.7k
Norway
iraun3.7k wrote:

If I've understood correctly your question, I'd suggest you the following workflow:

  1. Take the positions of those unannotated SNP.
  2. Create a bed file with:

    SNP_chromosome    SNP_position-10000    SNP_position+10000
    
  3. Create gene .bed|.gtf|.gff3 file with gene coordinates.
  4. Intersect (bedtools intersect) these two files.
ADD COMMENTlink modified 5 months ago by RamRS27k • written 4.4 years ago by iraun3.7k
0
gravatar for Emily_Ensembl
4.4 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

You can use the Ensembl VEP for this. To get variants 10kb up and downstream you'll need to alter the upstream/downstream distance to 10kb, which you'll find in the options.

ADD COMMENTlink written 4.4 years ago by Emily_Ensembl20k
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