How to convert a whole genome gene position reference number (ID) list to the actual text gene names?

Question

[lukdubofkremlin]

How to convert a whole genome gene position reference number (ID) list to the actual text gene names?

I have the NextGene output with POS ID column (.vcf, csv). Need toreturn tuberculosis genome gene symbols.

Answer 1

[mehran.karimzade]

Make sure our file is sorted and the first 3 columns of your file are: chromosome name | start position | end position

You would need to download a file from ENSEMBL biomart for your genome of interest that starts with first 3 columns as chromosome name | start position | end position | gene name ..... (this must be sorted too)

Then you would need to use bedtools to merge them by -intersect option.