List of genes TO starting and ending bps USING biomaRt R

Question

[Abdul Rafay Khan]

I have list of genes in a text file, I want to get the starting and ending bps location using biomaRt R.

Answer 1

[Bastien Hervé]

You have all the tools you need in your question (gene list, get start location, biomaRt)

If you google it, the first link is what you are looking for : https://support.bioconductor.org/p/28470/

[Abdul Rafay Khan]

Thank you for helping

gene_names=c("CYP3A5","CYP3A4")
mart<-useDataset("hsapiens_gene_ensembl",useMart("ensembl"))
getBM(c('hgnc_symbol','chromosome_name','start_position','end_position'),filters='hgnc_symbol',values=gene_names,mart)

[Bastien Hervé]

You're welcome. Is this solve then ?

To read a list of gene inside a file you can use :

gene_names <- scan(file = "your_file.txt", sep = "\n")

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