Using Liftoff for gene annotation

[suyeonwy]

Hi!

I am working on gene annotation for the newly assembled genome of a new pig breed.
I thought that the gene annotation of the pig reference genome could give useful information for annotating the genome of another breed of pig.
So I used Liftoff to map the annotation of the pig reference to the genome of the new breed.

And now, I am planning to merge the liftoff annotation with other annotations generated by different methods (RNA-seq based method, de novo method) with EvidenceModeler.
As I checked a manual for EVidenceModeler, they recommend using spliced alignments (intron-aware alignments, with evidence for intron and exon structures) as input.

Do you think that it would be fine for using the results of liftoff for this purpose?
I really appreciate any help you can provide.