[ensembl-dev] How to load sequences representing different phases of a diploid?

Thibaut Hourlier thibaut at ebi.ac.uk
Tue Oct 17 10:24:12 BST 2017


Hi Dan,
Yes it is the best solution in the actual schema. We have ‘haplotype’ which might be better, it works the same but with a different name. If there is a new assembly, an assembly patch would be part of the new assembly.  The relationship is only based on the reference. If you have: reference, phase1, phase2 you will be able to show: reference <-> phase1, reference <-> phase2. But I don’t think you will be able to show phase1 <-> phase2 on the website. In theory the API can probably manage phase1 <-> phase2 but I don’t think we’ve ever tried it.

Thanks
Thibaut

> On 16 Oct 2017, at 15:08, Dan Bolser <dbolser at ebi.ac.uk> wrote:
> 
> 
> 
> On 16 October 2017 at 14:40, Dan Bolser <dbolser at ebi.ac.uk <mailto:dbolser at ebi.ac.uk>> wrote:
> Hi,
> 
> We have a genome assembly where several scaffolds have been identified as different phases of a *heterozygous* diploid individual.
> 
> Spell chequer FTW!
> 
> 
> How best to represent these in Ensembl? As assembly patches?
> 
> 
> Many thanks,
> Dan.
> 
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