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UTR annotation on top of reference GTF

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"?

rna-seq
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updated by Ram Ram • written by rmihael • rmihael

Yes your assumption is right.

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written by Juke34 Juke34

1 answer

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)
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updated by Ram Ram • written by Devon Ryan Devon Ryan

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!

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updated by Ram Ram • written by craigmonger • craigmonger

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