Entering edit mode
3.7 years ago
xinhui.wang
▴
550
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
Please use the formatting bar (especially the
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), 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.ID's with
ENSMUST
are already Ensembl transcript ID's.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?
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.
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