gene ID translation

Question

[xinhui.wang]

Hi all,

I have some mouse gene expression data and the annotation is like

"uc009uap.1" , "ENSMUST00000167047" ,  "uc007fpb.1"          
"uc008pdt.1",  "MM9LINCRNAEXON11601-", "ENSMUST00000156438",  
"NR_002858", "uc008fcn.1",  "uc009vci.1"           "uc008lyy.1" 
,"AK029733",  "ENSMUST00000124572" ,  "ENSMUST00000124572",  
"NR_028109" ,   "NR_028109".

I would like to get the ensembl_transcript_id for all the seqs. Is there some R packages could help to do that?

Thanks and with best regards,

Micheal

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[GenoMax]

ID's with ENSMUST are already Ensembl transcript ID's.

[xinhui.wang]

yes. I am wondering could I find the ENSMUST ID's for "uc009uap.1" and "NR_028109", etc? Or is there easy tools could get ensembl_transcript_id from the RNA expression data?

[GenoMax]

I don't think Ensembl maps UCSC ID's directly so you may have to go through UCSC --> NCBI --> Ensembl. As for NCBI ID's those should be mappable using biomaRt package.

[xinhui.wang]

I am trying the BiomaRt package, however, I have no idea how to convert from UCSC to NCBI, do you have idea? foo <- getBM(attributes=c('ensembl_gene_id', 'external_gene_name','start','end'),filters = "ucsc",values = ss2, mart = ensembl) e