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Question about TransDecoder ORF score #201
Description
Hello,
Is there a way to interpret the ORF score from TransDecoder?
As far as I understand from here, TransDecoder predictions and performance are dataset-dependent and cannot be generalized. However, I wonder whether there is a minimum score value one can expect from an ORF to be considered a "reliable" enzyme-coding sequence?
I am working on de novo transcriptome assembly data (short RNA-Seq) from plants and the reason why I am asking is that I observed a high number of ORF with score below 1 (see figure below, more details on this Biostar post). So I was wondering whether I could filter those out, or at least flag them as "unreliable"?
Activity
mpizzagalli777 commentedon Jan 16, 2025
Hi titodamiani,
Did you ever get an answer to this question? I was wondering the same thing.
titodamiani commentedon Jan 17, 2025
Hi,
Not from the TransDecoder team, but in the meanwhile I discussed it with a few people working on RNA-Seq data. Overall, filtering data can be risky depending on your research question and type of sequences you're after. What I would recommend is to pick coding sequences (cds) in your data you're sure about (e.g., known ubiquitous genes) and see what their ORF score is and "develop a feeling" for it. In my case, I observed actual cds to have scores around 10+, but sometimes chopped csd (e.g., 3'- and 5'-partial) can be assigned lower scores and still could be relevant for your research question. Overall, I think when the score is below 1, it starts to be very unreliable and could in principle be filtered out. But again, it depends on your research question.
Hope this helps!
mpizzagalli777 commentedon Jan 17, 2025
HI, Thanks so much for your quick reply! That is very helpful for me and thanks for the suggestion for looking at ranges of ubiquitous genes.