need to identify CDS (translation) for gene models predicted by Cufflinks and Stringtie

Question

[Ann]

I have transcript models in GTF format made from assembling RNA-Seq read alignments using stringtie and also cufflinks. The reference genome is a new blueberry assembly I'm helping to annotate.

For the next steps, I need to find the genomic coordinates of the start and end of translation for the longest open reading in each transcript model.

Is there a program that can help me do that?

Previously, some-one in my group used a perl program called Tau to do this, but I don't have a copy of it. (Embarrassing!)

It seems like a straightforward task. Surely some-one has written something like this and put it on github or somewhere?

If not, do you think this would be a good project for a student learning bioinformatics?

[Kanoo]

Hi, I encountered a problem similar to what you described. I need to find the CDS (start/end codon) in my transcript models in GFF3 format. Have you solved it? Anyway, thanks!

Answer 1

[Chirag Nepal]

You could try transdecoder.