Question

CDS prediction for newly assembled transcripts

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7.3 years ago

I0110 ▴ 160

I am using stringtie for a reference-guided transcriptome assembly. For all of the isoforms with novel junctions or other novel transcripts, how can I predict the potential CDS? Is there a tool available for this? Thanks!!!

RNA-Seq transcriptome Assembly CDS • 3.5k views

ADD COMMENT • link updated 18 hours ago by Ales ▴ 20 • written 7.3 years ago by I0110 ▴ 160

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Transdecoder is popular for this purpose.

ADD REPLY • link 7.3 years ago by GenoMax 153k

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more tools: Best command line ORF finder

ADD REPLY • link 7.3 years ago by I0110 ▴ 160

score 2 · Answer 1 · 2025-09-07

We have recently developed a dedicated method ORFanage to address this specific issue in studies which already have detailed protein reference annotations (such as human, mouse, and other model organisms). Unlike other methods, it specifically aims to search for proteins that are most similar to those provided in the reference. Otherwise, if reference information is poor or unavailable, TD2 (successor to transdecoder) is a good choice!