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?