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

[Dan Bolser]

Thanks Thibaut,

I was also thinking that we could just put all the sequence / genes in as
normal, then flag them as 'components' of the same genome for Compara. I
think the only practical concern of having 'duplicated' phases is that
Compara will think these are duplicate genes. However, if we flag them as
components, it /should/ 'do the right thing'^{tm}.

On 17 October 2017 at 10:24, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:

> 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> 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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