What is the recommended way to group transcripts by "gene"? For example, rnaSPAdes returns a predicted gene identifier with the transcript in the identifier.
Is there a way to merge similar transcripts from different assemblies?
I'm sure this uses the graph files in the backend so what I'm asking may be really out of scope. I could use something like CD-HIT but I'm wondering if there was a better way. Maybe a way to use the de brujn graphs together?