Question: ncRNA search using biomaRt
0
gravatar for Zhang,Jiexin
3.7 years ago by
Zhang,Jiexin20
United States
Zhang,Jiexin20 wrote:

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

 

biomart ncrna • 496 views
ADD COMMENTlink modified 3.7 years ago by Thomas Maurel770 • written 3.7 years ago by Zhang,Jiexin20
Answer: ncRNA search using biomaRt
0
gravatar for Thomas Maurel
3.7 years ago by
Thomas Maurel770
United Kingdom
Thomas Maurel770 wrote:

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

ADD COMMENTlink written 3.7 years ago by Thomas Maurel770
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