Getting The Number Of Chromosome From Gene Id For A Lot Of Genes

Question

[thjnant]

Hello,

I have a vcf file that instead of the number of the chromosomes, I have the gene IDs, such as this:

ENSGALG00000000011|ENSGALT00000000012|57|1123|1125
ENSGALG00000000011|ENSGALT00000000012|57|1123|1125 ENSGALG00000000011|ENSGALT00000000012|57|1123|1125

I want to know to which chromsome each of these gene IDs belong and extract all the genes that belong to the Z or W chromosome. Indeed, one way is to search for each gene ID in Ensemble but there are more than 7000 genes. I was wondering whether there is any automatic way of doing this.

Thank you very much in advance, Cheers, Sandra

[Neilfws]

The answer to most "map ID X to ID Y" questions is BioMart; see answer from lelle and numerous other answers at this site.

Answer 1

[lelle]

You can use the Ensembl Biomart Instance to do this

• go to: http://www.ensembl.org/biomart/martview/
• select your organism
• add a filter with your gene IDs
• select the chromosome name as a attribute

[Sam]

You can extract all the gene IDs by using awk

awk -F "|" '{for(i=1;i<=NF;++i){print $i}}' input

You can get all the gene id this way (Assuming your input contain only what you've shown here) Then you can use those for biomart and quickly get the conversion as lelle stated