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

[Alessia Virzì]

Hello,

Thank you for this info.
I encountered some issues in cell type clustering (after snRNAseq) using this version you mentioned (Ensembl 113). While mapping on the NCBI NIH versions (V2 and V3) the clustering improved a lot.

Do you believe it can be something related to this problem you have highlighted?


Did someone encounter similar issues or other mismatch between gtf fasta files?


Thank you

Best regard,


Alessia Virzì

PhD | Postdoctoral researcher

Laboratory of Experimental Cardiology

Department of Cardiovascular Sciences

KU Leuven

________________________________
From: Dev <dev-bounces at ensembl.org> on behalf of Jorge Batista da Rocha <jrocha at ebi.ac.uk>
Sent: Monday, February 10, 2025 1:06 PM
To: Ensembl developers list <dev at ensembl.org>
Cc: helpdesk at ensembl.org <helpdesk at ensembl.org>
Subject: Re: [ensembl-dev] [Ensembl #791073] Mix of Ovis aries strains

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.

Ovis_aries_rambouillet - Ensembl genome browser 113<https://www.ensembl.org/Ovis_aries_rambouillet/Info/Index>
ensembl.org<https://www.ensembl.org/Ovis_aries_rambouillet/Info/Index>
<apple-touch-icon.png><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 <
> 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/

_______________________________________________
Dev mailing list    Dev at ensembl.org
Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
Ensembl Blog: http://www.ensembl.info/


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20250211/750dc8e7/attachment-0001.html>