I have a set of annotated genes in gff3 format and corresponding RNA-seq data. What is the recommended approach and are there specific tools and parameters to determine the percentage of genes supported by the RNA-seq data?"
To check for support of gene models by RNAseq, there are several proven workflows. I recommend using them all:
Standard RNAseq analysis based on alignments: Reference-based alignment by Hisat or STAR -> featureCounts/HTseq/RSEM -> check the coverage of the gene models of interest. There is no universally accepted cut-off for the number of reads or coverage per gene.
If you are interested in a computationally fast approach that also quantifies transcript isoforms (relevant if more than a single isoform is annotated in your GFF) use either Salmon or Kallisto
Use reference-guided transcriptome assembly (e.g. in Trinity) and Blast the transcripts. Check for overlaps of transcripts with gene-models
Visually inspect genes of interest for anomalies like shadowing, overlapping genes, duplicated sequences, inhomogeneous coverage, etc.
You could also do transcriptome assembly and then map the transcripts on the annotation via MAKER that will add an AED score for concordance between evidence (here transcript) and the annotation. AED=0 is perfect concordance, AED of 1 is complete absence of support.