[maker-devel] Apply old maker gff to new assembly

[Boyher, Adam]

Thank you Carson. That helps.

Can I ask another question in this thread? 
I have a phased genome (i.e. haplotype specific chromosomes of a
diploid organism). I'm debating on the best way to annotate. Does it
make sense to annotate both phases together, or separately? I've
previously annotated them separately, and found some genes that exist
on both phases are only annotated on one. I thought by annotating them
together, the second/third iterations using augustus and snap would
help annotate those missing genes. Another question I have is about
creating a "global" gene naming scheme. Meaning, I want genes that
exist on both phases to be named the same on both annotations,
global_0001 for instance, and genes that only exist on one phase to be
named a different way, phase0_0001. Do you have ideas on the best way
to do that?

Thanks for your help and time!
Adam



On Mon, 2019-12-02 at 11:42 -0700, Carson Holt wrote:
> Here is an archived post that covers this topic —> 
> https://groups.google.com/forum/#!searchin/maker-devel/est_forward%7Csort:date/maker-devel/gDbvTknuep4/gDiGCMgjCQAJ
> 
> This will help map old structural models to new coordinates. Moving
> functional data may take some additional work. You might even want to
> rerun domain finders like interproscan rather than just copying old
> domain coordinates.
> 
> —Carson
> 
> 
> > On Nov 15, 2019, at 2:26 PM, Boyher, Adam <
> > ABoyher at danforthcenter.org> wrote:
> > 
> > Hi
> > I'm a bit unsure of how to apply a previous maker annotation to a
> > new
> > assembly. I just want a quick annotation, so just taking the genes
> > that
> > are already in the annotation file with their functional
> > annotations
> > and naming schemes and find those genes in the new assembly. Which
> > settings should i use in maker_opts.ctl?
> > 
> > Thanks
> > Adam
> > _______________________________________________
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> > maker-devel at yandell-lab.org
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> 
>