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Alternative plan:
I have always known Trinity as de-novo transcriptome assembler.
Trinotate, part of the broader Trinity workflow, performs functional annotation: https://github.com/griffithlab/rnaseq_tutorial/wiki/Trinotate-Functional-Annotation
Thanks. I will go through that.
If you have a reference available then you are likely not doing gene prediction. And if you don't then you should be assemblig the data as suggested by @Michael.
We have assembled the genome and there is no other annotation available for this species. We have rnaseq and isoseq for some tissues. Currenlty figuring out the way I should prepare the files.
Was the genome assembly done independent of the RNAseq data? What do you mean by "prepare the files"?
Yes, independent of the RNAseq data. I mean gathering the evidence for the gene prediction by utilizing the RNAseq and isoseq data.
The RNAseq data should be assembled with trinity and transcripts to be given as input to tools like augustus, genemark etc or they should be mapped to genome with tools like hisat2/tophat and generate models with stringtie/cufflinks and later given as input to augustus, genemark etc.