I am looking to analyze the metatranscriptome of bacteria found on plants. I have sequenced my samples using nanopore and I've performed an assembly using Trinity and annotated them with Trinotate (default settings) against the uniprot-swisprot database. However, out of the thousand transcripts, only 10 were annotated.
I thought of trying to use Trinotate against a different database like the nr database to improve my annotation. Does anyone have any other suggestions or thoughts on how to improve the annotation output?
I really appreciate any advice.