Haplotype specific annotations

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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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Re: Haplotype specific annotations

Carson Holt-2
It may be that there are broken splice donors/acceptors in one vs the other which would not be seen with a blast search. Look at both in a browser to see what evidence looks like in both and how ab initial predictions compare between the two.

As for naming you could try reciprical best blast hits to see who matches who. Unfortunately you will have to do a lot of manual review to make sure you are not just matching parlors together.

—Carson

On Aug 28, 2019, at 12:31 PM, Boyher, Adam <[hidden email]> wrote:

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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