Is there any script to select longest ORF instead longest transcript from all assembled transcripts by Trinity?

Question

[seta]

Hi everybody,

As you all know, Trinity usually generate many transcripts. Given longest transcript is not always the best one. I'm looking for a script or tool that can select the longest ORF instead longest transcript among all generated transcripts by Trinity. Please let me know if there is such a script? Thanks

Answer 1

[Damian Kao]

TransDecoder will find best transcripts via ORF, hexamer frequency, blast, pfam:

https://transdecoder.github.io/

[seta]

Yeah, thanks.

Answer 2

[x.jack.min]

http://proteomics.ysu.edu/tools/OrfPredictor.html will work for you