Question: SNPs in Promoter region
0
gravatar for fatma.mokhtar
17 months ago by
fatma.mokhtar20 wrote:

Dear all, I want to select SNPs of specific genes in promoter region, how to do that?

Thanks in advance

snp • 508 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by fatma.mokhtar20

As a general rule of thumb: if your question fits in one sentence, you did not explain it sufficiently. Please see Brief Reminder On How To Ask A Good Question It is unclear which data you have, which file format you are using, which organism you are studying. Please elaborate.

ADD REPLYlink modified 17 months ago • written 17 months ago by WouterDeCoster44k

Thank you all for your replay,

I will formulate my question,

I have selected some genes and from those genes, I have downloaded their SNPs from Ensembl in Excel file. I want to select SNPs with high frequency in the European population with a minor allele frequency (MAF) between (0.24-0.49) but from that file, I couldn't find the SNPs that are in the promoter region?

Regards,

ADD REPLYlink written 17 months ago by fatma.mokhtar20

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

ADD REPLYlink written 17 months ago by WouterDeCoster44k

I have downloaded their SNPs from Ensembl in Excel file

There are two things wrong here:

  1. Excel is not an appropriate tool for genomic data analysis
  2. You did not tell us in which format these variants are: vcf, bed, something else?
ADD REPLYlink written 17 months ago by WouterDeCoster44k

https://www.ensembl.org/biomart/martview/5750b8dcd08b12d040ed5727b7bab963

From BioMart (Ensembl) I have downloaded the data in an Excel sheet. What is the appropriate way to download it?

ADD REPLYlink written 17 months ago by fatma.mokhtar20
1
gravatar for MatthewP
17 months ago by
MatthewP780
China
MatthewP780 wrote:

Hello, you need to first get coordinate/position of the promoter region from gff/gtf file on Ensembl. Then you need to extract all SNPs on that region from dbSNP with tool tabix. I hope this can help you. Last, you need to ask question with more detials, your question is too broad.

ADD COMMENTlink written 17 months ago by MatthewP780

Dear MatthewP, Thank you for your reply, but how to do those steps?

ADD REPLYlink written 17 months ago by fatma.mokhtar20

Dear Matthew,

How could I coordinate/position of the promoter region from gff/gtf?

ADD REPLYlink written 17 months ago by fatma.mokhtar20
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