PacBio transcriptome and gene annotation

Question

[Alex]

I have:

1) well assembled PacBio only genome with related organism with well annotated genes

2) Illumina transcriptome

3) PacBio transcriptome

4) Not so good as expected genes annotation with Maker and Illumina transcriptome

Do you try use PacBio transcriptome for gene annotation with Maker or any other tools?

I'm going to try following approaches:

1) Maker + PacBio transcriptome as is

2) GeneMakerS-T with PacBio transcriptome to get genes model

Any other ideas or hints?

[apelin20]

I am curious, what is the difference in number of assembled transcripts when comparing pacbio to illumina? Can you get at least 1 pacbio read for every illumina build transcript?