Regarding valid transcript and Transdecoder output

Question

[seta]

Hi all,

I have recently studied this paper that says in order to discriminate between valid transcript sequences and incorrectly assembled sequences, we used TransDecoder program. I know the usage of Transdecoder program, but I'm not sure about the above sentence. Could you please clarify me about the valid transcripts and Transdecoder tool? The author's mean is each transcript doesn’t translate to amino acid sequence is considered as incorrectly assembled transcript?

Thank you in advance

Answer 1

[ponganta]

From the paper you provided, I think it's not clear what the authors did with Transdecoder. Did they only retain putative coding transcripts? Was their wording imprecise?

In their methods the authors state, that they used assembled transcripts for quantification. Who knows.