Creating gtf file?

Question

[codsorre]

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

[opplatek]

What do you need a gtf for and what kind of information do you think it should contain? Since you have transcriptome assembly, a gtf in your case could be only used to describe CDS region and you already have that in the longest_orfs.gff3. The situation would be different if you had an assembled genome as well. In that case, you could map the assembled transcripts to the genome and then create a gtf which would describe UTRs, exons, CDS, ... But I guess you would have chosen to do a genome-guided transcriptome assembly instead which would most likely give you a gtf/gff right away..