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Hello,</div>
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Thank you for this info. </div>
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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. </div>
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Do you believe it can be something related to this problem you have highlighted?</div>
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Did someone encounter similar issues or other mismatch between gtf fasta files? </div>
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Thank you</div>
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Best regard,</div>
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<span style="font-family: Calibri, sans-serif; font-size: 12pt; color: rgb(36, 36, 36);"><b>Alessia Virzì</b></span></p>
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<span style="font-family: Calibri, sans-serif; font-size: 12pt; color: rgb(36, 36, 36);">PhD | Postdoctoral researcher</span></p>
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<span style="font-family: Calibri, sans-serif; font-size: 12pt; color: rgb(36, 36, 36);">Laboratory of Experimental Cardiology</span></p>
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<span style="font-family: Calibri, sans-serif; font-size: 12pt; color: rgb(36, 36, 36);">Department of Cardiovascular Sciences</span></p>
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<span style="font-family: Calibri, sans-serif; font-size: 12pt; color: rgb(36, 36, 36);">KU Leuven</span></p>
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<div id="x_x_divRplyFwdMsg" dir="ltr"><span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Dev <dev-bounces@ensembl.org> on behalf of Jorge Batista da Rocha <jrocha@ebi.ac.uk><br>
<b>Sent:</b> Monday, February 10, 2025 1:06 PM<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org><br>
<b>Cc:</b> helpdesk@ensembl.org <helpdesk@ensembl.org><br>
<b>Subject:</b> Re: [ensembl-dev] [Ensembl #791073] Mix of Ovis aries strains</span>
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<div style="direction: ltr;">Hi Sébastien,</div>
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<div style="direction: ltr;">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
<a href="https://www.ensembl.info/known-bugs/ensembl-113/" id="OWA640961ad-821d-e1e9-609b-ce1e8668da40" class="x_OWAAutoLink" data-auth="NotApplicable">
e!113 known</a> bugs. </div>
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<div style="direction: ltr;">The workaround is to use Texel files from the e!112 archive
<a href="http://may2024.archive.ensembl.org/Ovis_aries/Info/Index" id="OWAe713247b-b1f2-6e90-c256-56c9bdb2d6c0" class="x_OWAAutoLink" data-auth="NotApplicable">
http://may2024.archive.ensembl.org/Ovis_aries/Info/Index</a></div>
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<div style="direction: ltr;">Cheers!</div>
<div style="direction: ltr;">Jorge </div>
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<div style="direction: ltr;">Dr Jorge Batista da Rocha<br>
Ensembl Outreach Project Leader<br>
European Bioinformatics Institute (EMBL-EBI)</div>
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<blockquote>
<div style="direction: ltr;">On 6 Feb 2025, at 17:01, Jorge Batista da Rocha <jrocha@ebi.ac.uk> wrote:</div>
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<div style="direction: ltr;">Hi Sébastien, </div>
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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.</div>
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<a href="https://www.ensembl.org/Ovis_aries_rambouillet/Info/Index" id="OWAc15af6d1-78f3-f8bf-f7c9-2ad55871ccef" class="x_OWAAutoLink" data-auth="NotApplicable" style="text-decoration: none;">Ovis_aries_rambouillet - Ensembl genome browser 113</a></div>
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We’re still looking into the sheep FTP files, hope to get back to you soon. </div>
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Cheers! </div>
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Jorge</div>
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<div style="direction: ltr;">Dr Jorge Batista da Rocha<br>
Ensembl Outreach Project Leader<br>
European Bioinformatics Institute (EMBL-EBI)</div>
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<blockquote>
<div style="direction: ltr;">On 6 Feb 2025, at 13:23, Sebastien Moretti <</div>
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<div style="direction: ltr;">Thanks, waiting for your answer about the FTP.<br>
<br>
Does it mean the reference breed is Texel, and not Rambouillet, at Ensembl?<br>
The reference at RefSeq is now Rambouillet ARS-UI_Ramb_v3.0/GCF_016772045.2<br>
https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=9940<br>
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Best<br>
Sébastien<br>
<br>
On 06.02.2025 10:30, Jorge Batista da Rocha via RT wrote:</div>
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<div style="direction: ltr;"><URL: http://helpdesk.ebi.ac.uk/Ticket/Display.html?id=791073 ><br>
Dear Sébastien,<br>
Hope you are well! There have been some issues with the 113 release related<br>
files due to sheep texel getting switched up with ramboulliet when pipelines<br>
called for sheep - ovis aries.<br>
We know this affects VEP for sheep, we have a known bug for this- https://<br>
www.ensembl.info/known-bugs/ensembl-113/<br>
We are exploring the data on FTP and will get back to you, but until then, the<br>
workaround will be to use the files from the 112 release. https://<br>
ftp.ensembl.org/pub/release-112/json/ovis_aries/<br>
Thanks and best regards<br>
Jorge</div>
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--<br>
Sébastien Moretti<br>
Staff Scientist<br>
Department of Ecology and Evolution,<br>
Biophore, University of Lausanne,<br>
CH-1015 Lausanne, Switzerland<br>
Tel.: +41 (21) 692 4221<br>
https://bioinfo.unil.ch/ https://www.bgee.org/ https://selectome.org/<br>
<br>
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