Finding ORFs from RNA-seq Sequence Data of eukaryotic species

Question

[shome]

Hi, I am trying to find tools that can help me find ORFs from RNA-seq data.I could find many tools for prokaryotic species, but are there any available for eukaryotes?

[i.sudbery]

Do you mean from the transcript sequences, or from the transcribed regions annotated on the genome?

Answer 1

[lieven.sterck]

finding ORFs in transcripts is not much different from pro to eukaryotes. In theory any of the prokaryotic tools will also identify ORFs in eukaryotic transcripts, though some higher precision might be expected from a tool specifically designed for either one of them.

What you have found so far?

some pointers: TransDecoder, FrameD+ (has prokaryotic and eukaryotic mode), getORF, ... . There will also be some online resources around if you don't have to process too many transcripts.

[Dunois]

I'd add GeneMark-ST, orfipy, and CodAn to the list as well. The orfipy paper also mentions some older ORF prediction tools (including TransDecoder, getorf, and OrfM). Probably worth mentioning Plass as well if all OP wants to do is just get the proteome(s) from their RNA-seq data.