2
$\begingroup$

I am new to the field of Bioinformatics. Single Nucleotide Polymorphism or SNP data are available on the the Internet to download.SNP related data are valuable for variety of reasons ranging from disease related charatertcics and precision medicine to name the few.

Can somebody explain me the steps of downloading this kind of data from NCBI or other resource. For example if I want to download the the SNP in bunch of humans on a particular Gene from the specific start to end. What are the sequence of steps I would do online to download such data?

Update

I want SNP data for example for a particular gene say X from positions in range say base pairs 100,000 to 200,000 for individuals say 100 in txt or csv format or standard format that is available?

Like if I choose Gene X and position ranging from 100 to 109 base pairs in 5 persons I want following kind of data in txt or csv format with say two SNV at position 101 and 109

  1. A A A A A G G G G G
  2. A G A A A G G G G A
  3. A A A A A G G G G A
  4. A A A A A G G G G A
  5. A G A A A G G G G G

regards

$\endgroup$
2
  • 2
    $\begingroup$ What kind of data would you need? Just the SNP position and alternative sequence? The frequency of occurrence of each SNP in different populations? What format? rsIDs? VCF files? Something else? Please edit your question and make it more specific. $\endgroup$
    – terdon
    Apr 7 '18 at 15:17
  • $\begingroup$ @terdon please see updated Question $\endgroup$
    – Naseer
    Apr 8 '18 at 7:32
2
$\begingroup$

I would recommend to do this in R, using biomaRt.

For example if you want all the SNPs from IDH1 (ENSG00000138413) gene:

library(biomaRt)

ensembl<- useMart("ensembl")
ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)

IDH1 <- getBM(attributes=c('ensembl_gene_id','variation_name'), filters = 'ensembl_gene_id', values ="ENSG00000138413", mart = ensembl)

IDH1

You can add much more information, take a look at the help page of biomaRt.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.