CAT can't find gene duplications #317
Description
Hi,
I'm annotating 5 drosophila species (Chymomyza's) with Scaptodrosphila lebanonensis as a reference annotation and protein hints generated by miniprot but I don't have RNAseq for theses set of species . I'm mainly interested in gene copy number variations between these species but CAT is unable to find denovo duplications in the target genomes. For ex. I know there's 3-5 duplicated copies of Argonaute-2 in these genomes but CAT reports only one, Could this be due to any alignment issues or the fact that Scaptodrosophila has only one Argonaute-2 ? I've tried "--global-near-best=0.25" but still getting only one copy of this gene. Could you please help me with this? Thanks!