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<p>Hi Benjamin,</p>
<p>Thank you for reporting this error with the sequence download
options. This behaviour is the result of a known issue where
variants are missing MAF data in the latest Ensembl release
(Ensembl 111). More information can be found on the known bugs
page on our blog:<br>
</p>
<p><a class="moz-txt-link-freetext" href="https://www.ensembl.info/known-bugs/ensembl-111/">https://www.ensembl.info/known-bugs/ensembl-111/</a></p>
<p>This data will be available again in Ensembl 113, which is due to
be released later this year. In the meantime, we suggest using the
Ensembl 110 archive
(<a class="moz-txt-link-freetext" href="https://jul2023.archive.ensembl.org/index.html">https://jul2023.archive.ensembl.org/index.html</a>) to access this
data, as you have already found.</p>
<p>We apologise for any inconvenience.<br>
</p>
<p>Best wishes</p>
<p>Ben<br>
</p>
<div class="moz-cite-prefix">On 29/02/2024 21:14, Story Benjamin
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:462D9668-FECA-465C-BD51-A14D8B56CB48@chuv.ch">
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<p class="MsoNormal"><span lang="EN-US">Hi all,<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Not sure if this is the
right contact point for a bioinformatics bug (we have a
support ticket open via Fabienne Maurer but I’ve heard
progress is limited).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I’m writing this with
some potential critical implications. Our lab techs were
using Ensembl to extract gene sequences for designing Sanger
primers to validate variants in the parents of our pre-natal
patients. I’m not sure if we are alone in the world to do
the primer design this way or if it is just us.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Starting sometime after
December 28<sup>th</sup> (first fault detection on Jan 15<sup>th</sup>),
the rich text format (RTF) output from the main ensemble
website is no longer displaying any variant coloration when
you apply MAF filtering (potentially with release 111? Maybe
dbSNP related?).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Usually, we remove
highlighting from variants with a minor allele frequency
(MAF) of less than 0.01% to avoid rare variants so we can
solely visualize the common polymorphisms. Otherwise, we
risk designing a primer which could provide a false-negative
result for a patient/parent (i.e. if one of the primers fail
to anneal due to inherent variation in the population).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Currently when the MAF
< 0.01% filter is applied all “coloration/highlighting”
(i.e. a proxy for MAF) for the variants is NOT output to the
RTF file.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Luckily, I’m aware of
the Ensembl archives and this was able to solve our
immediate problem.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">However, in case anyone
else is using a similar method I think it would be good to
fix the underlying issue.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Steps to reproduce:<br>
<br>
<o:p></o:p></span></p>
<ol style="margin-top:0cm" type="1" start="1">
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level1 lfo3"><span
lang="EN-US">Visit transcript exon page.<o:p></o:p></span>
<ol style="margin-top:0cm" type="a" start="1">
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level2 lfo3"><span
lang="EN-US">Working :
<a class="moz-txt-link-freetext" href="http://jul2023.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000075624;r=7:5526409-5563902;t=ENST00000646664">http://jul2023.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000075624;r=7:5526409-5563902;t=ENST00000646664</a><o:p></o:p></span></li>
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level2 lfo3"><span
lang="EN-US">Broken:
<a class="moz-txt-link-freetext" href="http://ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000075624;r=7:5526409-5563902;t=ENST00000646664">http://ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000075624;r=7:5526409-5563902;t=ENST00000646664</a><o:p></o:p></span></li>
</ol>
</li>
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level1 lfo3"><span
lang="EN-US">Click ‘Download Sequence’ (just below
<o:p></o:p></span></li>
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level1 lfo3"><span
lang="EN-US">Set ‘File format’ to RTF (Word-compatible)<o:p></o:p></span></li>
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level1 lfo3"><span
lang="EN-US">For the option ‘Hide variants by frequency
(MAF)’ set it to ‘Hide rare, MAF < 0.01%’
<o:p></o:p></span></li>
<li class="MsoListParagraph"
style="margin-left:0cm;mso-list:l0 level1 lfo3"><span
lang="DE-CH">Click ‘Download’<o:p></o:p></span></li>
</ol>
<p class="MsoNormal"><span lang="DE-CH"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If you start with 1a you
get a sequence with highlighted variants based on MAF (with
the rare ones excluded, i.e. un-highlighted)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If you start with 1b you
don’t have any significant highlighting.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Note that if you don’t
apply step 4 you get all the highlighting for all variants
regardless of MAF (which still works for both 1a and 1b) –
suggesting its related to the filtering.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I tried on multiple OS,
browsers, computers, ensembl-mirrors, and the issue seems to
stem from the v111 release.<br>
<br>
Hope this helps.<br>
<br>
Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Ben<o:p></o:p></span></p>
</div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr. Ben Moore (he/him)
Ensembl Outreach Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
<a class="moz-txt-link-abbreviated" href="mailto:bmoore@ebi.ac.uk">bmoore@ebi.ac.uk</a>
+44 (0)1223 494265</pre>
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