[maker-devel] Haplotype specific annotations

[Boyher, Adam]

Hi

I have a phased genome (haplotype specific assemblies) that I have annotated separately with Maker. There are a couple of things I’ve had a little trouble figuring out in relation to this. The first is that I have 3 sets of genes, two sets that exist in one haplotype but not the other, and a third that exist in both. I want to name these genes specifically based on what set they are in. So for instance, genes that exist in both have the same name in both assemblies, but genes that exist in only one haplotype are named specific to that haplotype. Is there a straightforward way to do this?

The second issue is that I’ve discovered one gene that is annotated in one phase, but not the other. However, when I blast the genomic sequence against the second haplotype, I find an exact match. Given that I used the exact same methods to annotate both haplotypes, starting with the same set of evidence (protein, transcriptome, repeat), why might maker miss or exclude that gene?

Thanks
Adam
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