UTR annotation on top of reference GTF

Question

[rmihael]

I'm trying to study UTRs based on reference genome of rattus norvegicus available at http://www.ncbi.nlm.nih.gov/genome?term=rattus%20norvegicus. Provided GTF has information about exons and CDS, so I'm wondering if there's any tools available that can automatically derive UTR annotation based on this data?

Also, if there's no such tools available, will it be correct to assume that UTR can be derived as "concatenation of all exons of a transcript excluding concatenation of all CDSs of same transcript"?

[Ashutosh Pandey]

A helpful post: Easy Way To Get 3' Utr Lengths Of A List Of Genes

[Juke34]

Yes your assumption is right.

Answer 1

[Devon Ryan]

In R:

library(GenomicFeatures) #You may have to install this
txdb <- makeTranscriptDbFromGFF("something.gtf", format="gtf") #this will take some time
fiveUTRsByTranscript(txdb)
threeUTRsByTranscript(txdb)

[craigmonger]

Just came across this helpful answer 2.5 years in the future.

Seems the command is now txdb<-makeTxDbFromGFF("something.gtf", format="gtf") for anybody in the future looking to achieve this!