[ensembl-dev] [Ensembl #791073] Mix of Ovis aries strains

[Jorge Batista da Rocha]

Hi Sébastien,

Thanks for raising this - there is an issue with Texel FTP files, and we aim to resolve this in our upcoming releases. We’ve also added a known bug for this on e!113 known <https://www.ensembl.info/known-bugs/ensembl-113/> bugs. 

The workaround is to use Texel files from the e!112 archive http://may2024.archive.ensembl.org/Ovis_aries/Info/Index

Cheers!
Jorge 

Dr Jorge Batista da Rocha
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)

> On 6 Feb 2025, at 17:01, Jorge Batista da Rocha <jrocha at ebi.ac.uk> wrote:
> 
> Hi Sébastien, 
> 
> Regarding the sheep reference - the reference sheep in Ensembl is Rambouillet, but to note, we are displaying data for ARS-UI_Ramb_v2.0, the previous version as compared to the refseq reference.
> 
> https://www.ensembl.org/Ovis_aries_rambouillet/Info/Index
> 
> We’re still looking into the sheep FTP files, hope to get back to you soon. 
> 
> Cheers! 
> Jorge
> 
> Dr Jorge Batista da Rocha
> Ensembl Outreach Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> 
>> On 6 Feb 2025, at 13:23, Sebastien Moretti <sebastien.moretti at unil.ch> wrote:
>> 
>> Thanks, waiting for your answer about the FTP.
>> 
>> Does it mean the reference breed is Texel, and not Rambouillet, at Ensembl?
>> The reference at RefSeq is now Rambouillet ARS-UI_Ramb_v3.0/GCF_016772045.2
>> https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=9940
>> 
>> Best
>> Sébastien
>> 
>> On 06.02.2025 10:30, Jorge Batista da Rocha via RT wrote:
>>> <URL: http://helpdesk.ebi.ac.uk/Ticket/Display.html?id=791073 >
>>> Dear Sébastien,
>>> Hope you are well! There have been some issues with the 113 release related
>>> files due to sheep texel getting switched up with ramboulliet when pipelines
>>> called for sheep - ovis aries.
>>> We know this affects VEP for sheep, we have a known bug for this- https://
>>> www.ensembl.info/known-bugs/ensembl-113/
>>> We are exploring the data on FTP and will get back to you, but until then, the
>>> workaround will be to use the files from the 112 release. https://
>>> ftp.ensembl.org/pub/release-112/json/ovis_aries/
>>> Thanks and best regards
>>> Jorge
>>>> Sébastien
>> 
>> --
>> Sébastien Moretti
>> Staff Scientist
>> Department of Ecology and Evolution,
>> Biophore, University of Lausanne,
>> CH-1015 Lausanne, Switzerland
>> Tel.: +41 (21) 692 4221
>> https://bioinfo.unil.ch/ https://www.bgee.org/ https://selectome.org/
>> 
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