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<p>Thanks Natalie for the explanation.</p>
<p>This is a BIG change that has the potential to break or hurt the
reproducibility of lots of code that makes use of these
annotations. Was this announced somehow or is there a document
somewhere on the Ensembl website that describes these changes?
Sorry in advance if I missed it.<br>
</p>
<p>Thanks again,</p>
<p>H.<br>
</p>
<div class="moz-cite-prefix">On 8/24/23 01:57, Natalie Willhoft
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:83724054-8774-4558-B654-1B48571A5747@ebi.ac.uk">
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<div dir="auto" style="overflow-wrap: break-word;
-webkit-nbsp-mode: space; line-break: after-white-space;">Hi
Hervé,
<div><br>
</div>
<div>Thanks for your email.</div>
<div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">
</span></div>
<div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">In previous releases, genes on patches were projected from their scaffold sequences (e.g. HSCHR6_MHC_APD_CTG1) and stored onto chromosome-based sequences (e.g. CHR_HSCHR6_MHC_APD_CTG1). Therefore in this case, the gene(s) on this example patch had been projected onto a sequence with coordinate positions in the context of human chromosome 6. Historically, the Ensembl Core Perl API was built to support genes on patches based on these chromosome-based sequences, which were ultimately used to visualise a given patch on the Ensembl Browser with all its associated features.</span></div>
<div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">
</span></div>
<div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">As you mentioned, this has changed as of Release 110 so that we now keep the genes (and their associated features) on their original scaffold patch sequence. I should also clarify that this work only relates to human.</span></div>
<div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">
</span></div>
<div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">Please do let us know if you have any more questions on this topic.</span></div>
<div><br>
</div>
<div>Thanks and best wishes,</div>
<div>Natalie</div>
<div><br>
<div>
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<div dir="auto" style="caret-color: rgb(0, 0, 0); color:
rgb(0, 0, 0); letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;
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<div dir="auto" style="caret-color: rgb(0, 0, 0); color:
rgb(0, 0, 0); letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;"><b>Natalie Willhöft (Dawson)</b><br>
Ensembl Infrastructure Team<br>
EMBL-EBI <br>
<a class="moz-txt-link-abbreviated" href="mailto:nwillhoft@ebi.ac.uk">nwillhoft@ebi.ac.uk</a></div>
</div>
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<blockquote type="cite">
<div>On 23 Aug 2023, at 06:30, Hervé Pagès
<a class="moz-txt-link-rfc2396E" href="mailto:hpages.on.github@gmail.com"><hpages.on.github@gmail.com></a> wrote:</div>
<br class="Apple-interchange-newline">
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<p>Hi,</p>
<p>Looks like starting with Ensembl 110 (now based on
GRCh38.p14), human gene ENSG00000231116 (VARS) is
now reported to be located on sequence
HSCHR6_MHC_APD_CTG1 after being reported to be on
sequence CHR_HSCHR6_MHC_APD_CTG1 for many years (at
least since Ensembl release 85, based on GRCh38.p7).</p>
<p>Anybody knows what sequence CHR_HSCHR6_MHC_APD_CTG1
was actually supposed to be? Was never a valid
GRCh38 sequence name. At least the new sequence name
belongs to GRCh38.</p>
<p>Thanks,</p>
<p>H.<br>
</p>
<pre class="moz-signature" cols="72">--
Hervé Pagès
Bioconductor Core Team
<a class="moz-txt-link-abbreviated moz-txt-link-freetext" href="mailto:hpages.on.github@gmail.com" moz-do-not-send="true">hpages.on.github@gmail.com</a>
</pre>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</blockquote>
<pre class="moz-signature" cols="72">--
Hervé Pagès
Bioconductor Core Team
<a class="moz-txt-link-abbreviated" href="mailto:hpages.on.github@gmail.com">hpages.on.github@gmail.com</a>
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