Entering edit mode
7.9 years ago
bsmith030465 ▴ 210
I was trying to extract the 5' UTR and 3'UTR coordinates for a particular isoform. My code is:
library(biomaRt) mart = useMart("ensembl") getBM(attributes = c("5_utr_start","5_utr_end","3_utr_start","3_utr_end"),filters = "hgnc_symbol",value = "AAGAB",mart = ensembl)
Is there a way that I can specify that for the gene (AAGAB), I want information for isoform 001 (ie. AAGAB-001)? Else, how do I process the data given by my query above so that I can get this information?
Or should I be doing something else altogether?
I suspect that specifying a query based on gene symbol is not the way to go. You'll probably need to specify a transcript in the filter. Do you know a transcript ID?
Thanks for the reply. So, if I want to get the details of "ENST00000538028", I should use something like:
Am I using the right filters?
Looks right. You might want to specify
ensembl_transcript_idin the attributes as well.
Indeed, a working example here: A: R org.Hs.eg.db matching ensembl gene ids with gene symbol