Extract Ensembl IDs column using a data file

Question

[mohammedtoufiq91]

Hi,

I have a normalized data file containing gene symbols as first column followed by various samples (normalized data). I was looking to extract the Ensembl IDs corresponding to the gene symbols. Basically, I would like to have both gene symbols and Ensembl IDs in the data file for further downstream analysis. Please assist me with this.

Current format

gene_symbol Sample_1 Sample_2

Revised format

gene_symbol Ensembl ID Sample_1 Sample_2

Best Regards, Toufiq

Answer 1

[c.chakraborty]

Use bioMart from bioconductor, to extract the ENSEMBL IDs of your genes.https://www.bioconductor.org/packages/devel/bioc/vignettes/biomaRt/inst/doc/biomaRt.html

Answer 2

[Erin Haskell | ELIXIR]

BioMart is definitely the way to go. You can use the R package Bioconductor as c.chakraborty suggests, or the point and click web tool. We have a video covering ID conversion that you may find helpful.

[mohammedtoufiq91]

Thank you. This was helpful.