So far, Approaches to GO annotation of transcriptomes of non-model organisms (besides B2G) point to the use of Trinotate and Genescf. I would like to ask if there is an easy way to directly add GO annotation to a diamond blast result (against NCBI nr)? Since B2G is really slow on a basic subscription, I would like to find a way to do GO annotation.
Also, here's my confusion right now: can I just use the GO annotation from Trinotate pipeline or do I really need to use the nr result for this since more sequences have annotations in nr? If using only trinotate (swissprot+eggnog+pfam), would I be missing some GO terms that may be recovered if I've used nr? Or will it be safe to just use interproscan GO result to represent the transcriptome instead?
Finally, what is the best way to convert the genbank protein IDs (XX#####.#) and RefSeq IDs (XX_#*) from diamond blast of a non-model organism, to say Gene name (e.g. FOLH, DUPD1)?