Biomart select rRNA sequences

Question

[Vlad]

I want to select all the ribossomal genes from mouse. I tried to use Rat Genome database rgd.mcw.edu) and select the ribossomal genes but some of the genes that are listed in my Sequencing results are not present there (such as Rps28 gene and some more). I am trying now to select from Biomart but I cannot find any attribute that can classify my Ensembl_id into for example mRNA, rRNA etc.

Is there a way to get all rRNA genes from biomart or is there a better library to achieve my goal?

Answer 1

[Mike Smith]

You can use the 'Gene Type' filter in Ensembl BioMart to restrict your results to a certain group. With the biomaRt package you'd do that via:

library(biomaRt)
mart <- useEnsembl('ensembl', dataset = 'rnorvegicus_gene_ensembl')
biomaRt::getBM(values="rRNA", 
               filters="biotype", 
               attributes=c("ensembl_gene_id", "external_gene_name", "gene_biotype"), 
               mart = mart)

However I don't see Rps28 listed as a rat gene on Ensembl, so it may be that you are encountering annotation & naming difference between different sources.

[jasonwufree2012]

It seems Ensembl is not a complete annotation of rRNA genes. There are only 5S and 5.8S in Human Ensembl. Correct me if I am wrong. Thx

Answer 2

[Vlad]

Works perfectly , thanks.