Trandecoder on output from braker2

[alexis groppi]

Hi,

I have run Braker2 with RNAseq and a close proteome fasta file on my plant genome.
My question is : is it a good thing to run Transdecoder on these results ?
Some week ago I have read a discussion about this but I can't find it anymore :/

Thanks for your advises

Alexis

[Brian Haas]

Hi,

I think Braker2 should be giving you coding region annotations as it's final output.  In this case, it would not make sense to run TransDecoder, since the coding regions are already defined.

TransDecoder is instead focused on identifying coding regions within transcript structures where coding regions are not already defined.  (ie. running StringTie, Trinity, etc., given rna-seq data)

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas