problem with assign novel isoforms to annotated gene

[Drosofriends]

Hi I have run scallop and I obtained a gtf with annotated and unique isoforms reconstructed by scallop. I want to know the gene ID associated to the novel isoform. How can I do this?
thanks for your help!

[shaomingfu]

Hi, Scallop gave a "gene ID" for each transcript, but I assume you are looking for the association with gene IDs from a reference annotation or a gene nomenclature. Scallop does not produce that. You may associate a predicted gene (by Scallop) to a known annotated gene by checking: (1) if the range (genomic coordinates) of the two genes overlap a lot, and (2) if two transcripts, one from each gene, share one or more identical intron-exon boundaries. -Mingfu