Hi,

I am using biomaRt to extract genomic locations for genes of interest. I found that it doesn't work on ncRNAs. For example, I have MRPL45P2 in my gene list, couldn't find anything.

> x <- 'MRPL45P2'

> addCol <- c('refseq_ncrna','chromosome_name','start_position','end_position','strand','band')

> getBM(attributes=addCol,filters=addCol[1],values=x,mart=ensembl)

[1] refseq_ncrna    chromosome_name start_position  end_position  

[5] strand          band          

<0 rows> (or 0-length row.names)

So I thought maybe I need to provide "NR_XXXX" value for it to work, still no.

> x <- 'NR_033934'

> addCol <- c('refseq_ncrna','chromosome_name','start_position','end_position','strand','band')

> getBM(attributes=addCol,filters=addCol[1],values=x,mart=ensembl)

[1] refseq_ncrna    chromosome_name start_position  end_position  

[5] strand          band          

<0 rows> (or 0-length row.names)

I even tried the one shown in user guide of biomaRt: NR_002834

> x <- 'NR_002834'

> addCol <- c('refseq_ncrna','chromosome_name','start_position','end_position','strand','band')

> getBM(attributes=addCol,filters=addCol[1],values=x,mart=ensembl)

[1] refseq_ncrna    chromosome_name start_position  end_position  

[5] strand          band          

<0 rows> (or 0-length row.names)

Would someone please give me some suggestions on how to do it?

Thanks a bunch,

Jiexin

Dear Jiexin,

The "refseq_ncrna" Ensembl gene mart filter only accept ids like "NR_XXXX" so this is why "MRPL45P2" is not working. I am afraid NR_033934 and NR_002834 returns nothing because these two ids are not mapped to any Ensembl Gene IDs at the moment.

Hope this helps,

Regards,

Thomas