Excuse me for lack of knowledge on this topic. I am currently trying to build a gene expression matrix and am needing one of the gene transfer files. I built a denovo transcriptome with trinity on sequenced samples so I am under the impression I need to build the gtf file (as its a nontraditional model organism and not widely available). I went through the steps of annotating the transcriptome with blast results and ran it with trinotate. I have the longest_orfs.gff3 file from transdecoder, but I don't feel like that is the right thing. Any help would be appreciated and happy to give any more information that I am sure you will need

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