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By using the site you are agreeing to this as outlined in our <a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice" rel=""> Privacy Policy </a> </div> </aside> </div> </div> </div> <div id="primary" class="content-area col-lg-9" itemprop="mainContentOfPage"> <div itemscope itemtype="http://schema.org/Article" id="content" class="site-content" role="main"> <article id="post-15719" class="post-15719 page type-page status-publish hentry"> <header class="entry-header"> <h1 class="entry-title" itemprop="name">Ensembl 113</h1> </header> <div class="entry-content" itemprop="articleBody"> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>Getting the wrong species alias for <em>Ovis aries</em> (Sheep) Texel</h3></td></tr><tr><td><strong>Affects: </strong>Live site</td><td><strong>Expected fix: </strong>Ensembl 114</td></tr><tr><td colspan="2"><strong><strong>Description: </strong></strong>In ensembl-vep we expect to get the species latin name using the aliases through the Bio::EnsEMBL::Registry::get_alias() function – <p>https://github.com/Ensembl/ensembl-vep/blob/eb55c2293637c34a0f80dfca88c439e77dd52def/modules/Bio/EnsEMBL/VEP/BaseRunner.pm#L143<span style="font-family: inherit;font-size: inherit;font-weight: inherit;color: initial"> </span>It is an old code but intuitively the idea is to able to run VEP using “–species sheep”. The scientific name which should be returned as ovis_aries would then be used to get proper database or cache files. If “–species ovis_aries” is used (which is the case for web VEP) get_alias() should return ovis_aries.In e113, using “–species ovis_aries” is returning “ovis_aries_rambouillet”.Affected VEP areas:<br>1. VEP cache: the sheep texel contains the data dumped from Rambouillet database.<br>2. Web VEP: gets the wrong cache and assembly version.<br>3. REST VEP: REST does not allow ovis_aries (why?) but allows ovis_aries_rambouillet as species name. To get results for sheep texel before e113, we could give “sheep” as species name and it would work but now sheep gives results<span style="font-family: inherit;font-size: inherit;font-weight: inherit;color: initial"> for Rambouillet</span><span style="font-size: revert;font-family: inherit;font-weight: inherit;color: initial">. So we cannot get results for sheep texel in e113.</span></p></td></tr><tr><td colspan="2"><strong>Workaround: </strong>Please use <a href="https://ftp.ensembl.org/pub/release-112/" target="_blank" rel="noopener">data from the Ensembl 112 archive</a>.</td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>Incorrect source project label for regulation data in cow<span style="font-family: inherit;font-size: inherit;font-weight: inherit;color: initial"> </span></h3></td></tr><tr><td><strong>Affects: </strong>Live site</td><td><strong>E<strong>xpected fix</strong>: </strong>Ensembl 114</td></tr><tr><td colspan="2"><strong>Description: </strong>Source data for cow e.g. [https://rc.ensembl.org/Bos_taurus/Regulation/Evidence?db=funcgen;fdb=funcgen;r=9:96621727-96624008;rf=ENSBTAR9_93FCH2] incorrectly lists ENCODE instead of FAANG.</td></tr><tr><td colspan="2"><strong>Workaround: </strong>There is currently no workaround, however, this bug is not known to affect downstream analyses.</td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>“Genotype: frequency (count)” does not match “Allele: frequency (count)”</h3></td></tr><tr><td><strong>Affects: </strong>Live site</td><td><strong>Expected fix: </strong>Ensembl 114</td></tr><tr><td colspan="2"><strong>Description: </strong>We observed the mismatch allele and genotype frequencies for a population on the variant genotype page. Allele frequency looks good however genotype frequency does not match with the allele frequency. </td></tr><tr><td colspan="2"><strong>Workaround: </strong>The table for sample genotypes also looks okay.</td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>Motif widget only shows human data<span style="font-family: inherit;font-size: inherit;font-weight: inherit;color: initial"> </span></h3></td></tr><tr><td><strong>Affects: </strong>Live Site</td><td><strong><strong>E<strong>xpected fix</strong></strong>: </strong>Ensembl 114</td></tr><tr><td colspan="2"><strong>Description:</strong> The <a href="https://widgets.ensembl.org/motif_feature.htm?id=ENSPFM0001" target="_blank" rel="noopener">Motif widget</a> only shows human data, even if it is accessed from other species’ pages.</td></tr><tr><td colspan="2"><strong>Workaround:</strong> There is currently no workaround.</td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3><span style="font-size: 18px;font-weight: 400"><strong><h3>Alignment artefact in some ncRNA homology and gene-tree alignments</h3></strong></span></h3></td></tr><tr><td><strong>Affects</strong>: Live site, Ensembl 100, Ensembl 101, Ensembl 102, Ensembl 103, Ensembl 104, Ensembl 105, Ensembl 106, Ensembl 107, Ensembl 108, Ensembl 109, Ensembl 110, Ensembl 111, Ensembl 112</td><td><strong>E<strong>xpected fix</strong></strong>: Ensembl 114</td></tr><tr><td colspan="2"><strong>Description: </strong><span style="font-size: revert;font-family: inherit;font-weight: inherit;color: initial">An alignment artefact has been detected in ncRNA homology and gene-tree alignments (e.g. [ENSBTAG00000045380|http://may2024.archive.ensembl.org/Bos_taurus/Gene/Compara_Tree?collapse=none;db=core;g=ENSBTAG00000045380]). In affected cases, the alignment sequence is generated from an unflanked ncRNA sequence and a CIGAR line of a flanked genomic alignment. This may result in the original sequence being followed by a sequence of ‘N’ ambiguity symbols, or in some cases, in an alignment composed entirely of ‘N’ ambiguity symbols.</span><span style="font-size: inherit;font-family: inherit;font-weight: inherit;color: initial"> </span><span style="font-size: revert;font-family: inherit;font-weight: inherit;color: initial">As of Ensembl 112, this issue affected 193,110 ncRNA genes and 31,987 trees. Ensembl 113 saw us take our first steps to mitigate this issue, as a result it affects 75,360 genes and 8,805 trees in that release.</span></td></tr><tr><td colspan="2"><strong>Workaround</strong>: There is currently no workaround.</td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>Age-of-Base file lacks data for chromosomes 1 to 7<span style="font-family: inherit;font-size: inherit;font-weight: inherit;color: initial"> </span></h3></td></tr><tr><td><strong>Affects: </strong>Live site, Ensembl 111, Ensembl 112</td><td><strong><strong>E<strong>xpected fix</strong></strong>: </strong>Ensembl 114</td></tr><tr><td colspan="2"><strong>Description:</strong> Due to a pipeline synchronisation issue, the Age-of-Base data file generated in Ensembl release 111 lacks a date for chromosomes 1 through 7.</td></tr><tr><td colspan="2"><strong>Workaround: </strong> For chromosomes 1-7, we recommend to access the Age-of-Base resource via the Ensembl 110 archive site.</td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>C-terminal ‘X’ missing from some Compara protein member sequences</h3></td></tr><tr><td><strong>Affects: </strong>Live site, Ensembl 112</td><td><strong><strong>E<strong>xpected fix</strong></strong>: </strong>Ensembl 114</td></tr><tr><td colspan="2"><strong>Description:</strong> For some protein sequences whose CDS ends with a partial codon (e.g. <a href="https://www.ensembl.org/Acanthochromis_polyacanthus/Gene/Summary?db=core;g=ENSAPOG00000012172" target="_blank" rel="noreferrer noopener">ENSAPOG00000012172</a>), the C-terminal ‘X’ which can be found in the translation in the core database was found to be absent from the sequence of the corresponding member in the Compara database. As of release 113, this issue affects 1,928 proteins in Vertebrates, 160 in Plants, 60 in Pan Compara, and 3 in Metazoa.<br>We aim to correct 95% of affected protein sequences in Ensembl release 114. The remaining affected protein sequences — in <em>Aegilops_tauschii</em>, <em>Oryza brachyantha</em>, <em>Oryza rufipogon</em> and <em>Triticum_dicoccoides</em> — will be fixed when we next update the protein trees for these species.</td></tr><tr><td colspan="2"><strong>Workaround:</strong> There is currently no workaround.</td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>Large number of ancient paralogies for Triticum aestivum Kariega in a Wheat cultivar supertree</h3></td></tr><tr><td><strong>Affects: </strong>Live site</td><td><strong>Expected fix: </strong>Ensembl 114</td></tr><tr><td colspan="2"><strong>Description: </strong>During preparation of Wheat cultivar protein trees for Ensembl release 113, it became apparent that supertree PTHR11439_SF127 has approximately 40,000 genes in Triticum aestivum cultivar Kariega. Generation of the 261 million ancient paralogies between these genes took two weeks, and it would not have been possible to include them in Ensembl Plants 113 without delaying the release.</td></tr><tr><td colspan="2"><strong>Workaround: </strong>A cross-section of the relevant ancient paralogies was loaded during production, involving genes with stable IDs TraesKAR6A01G0279700, TraesKAR7B01G0056390, TraesKAR7B01G0463280 and TraesKAR1D01G0304830. Due to the large number of paralogies involved, these may fail to load correctly on the Ensembl Plants website, though it should be possible to access them via the Ensembl REST API and Compara Perl API.<br><br>A file containing data on these 40,000 genes is available for download at the following location on the Ensembl Genomes FTP site:<br><a href="http://ftp.ensemblgenomes.org/pub/release-60/plants/emf/ensembl-compara/homologies/Compara.113.protein_wheat_cultivars.other_paralogies.cds.fasta.gz">http://ftp.ensemblgenomes.org/pub/release-60/plants/emf/ensembl-compara/homologies/Compara.113.protein_wheat_cultivars.other_paralogies.cds.fasta.gz</a></td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>Issues affecting Cactus alignments</h3></td></tr><tr><td><strong>Affects: </strong>Live site</td><td><strong>Expected fix: </strong>Timeline currently unknown</td></tr><tr><td colspan="2"><strong>Description: </strong>Long loading times were observed during testing of several Cactus alignments, so the following measures were adopted to mitigate this.<br>Cactus alignments accessed via the API are filtered to remove shorter alignment blocks. This may cause Cactus alignments to appear sparse when viewed at larger scales, so please view Cactus alignments at the smallest scale that allows for viewing the feature(s) of interest.<br>In the image alignment view, gene tracks are switched off by default for all but the current genome. In addition, alternative gene model tracks are switched off by default in the 16-Wheat Cactus alignment. Please switch on gene tracks as needed using the configuration bar at the top of the alignment view.<br>Because the 16-Wheat Cactus alignment was loaded separately for each component (A, B and D) and non-polyploid genomes were included in alignments for all three components, particularly long loading times were observed when viewing this alignment from non-polyploid genomes, so the Wheat Cactus has been removed from the alignment selection dropdown menu for non-polyploid genomes on the Ensembl Plants website. Their alignments can be viewed from the perspective of polyploid genomes.<br>In an issue unrelated to loading time, the 16-Wheat Cactus alignment has in effect 3 species trees — one per genome component — so this alignment has a single dummy species tree to facilitate access to the alignment, which is hidden from view on the Ensembl Plants website. The full Wheat Cactus species tree can be accessed via the Compara API or from the Plants species-tree location on the Ensembl Genomes FTP site: <a href="http://ftp.ensemblgenomes.org/pub/release-60/plants/compara/species_trees/16_wheat_Cactus_default.nh" target="_blank" rel="noreferrer noopener">http://ftp.ensemblgenomes.org/pub/release-60/plants/compara/species_trees/16_wheat_Cactus_default.nh</a><br>We aim to address these issues more comprehensively in Ensembl 114 and subsequent releases.</td></tr><tr><td colspan="2"><strong>Workaround: </strong>There is currently no workaround.</td></tr></tbody></table></figure> <figure class="wp-block-table"><table class="has-fixed-layout"><tbody><tr><td colspan="2"><h3>Incorrect allele and genotype frequency in Watkins Collection</h3></td></tr><tr><td><strong>Affects: </strong>Ensembl Plants 60</td><td><strong>Expected fix: </strong>Ensembl Plants 61</td></tr><tr><td colspan="2"><strong>Description: </strong>Approximately 1% of the wheat variants that were loaded from the Watkins Collection has an incorrect allele and genotype frequency. This results from sample overlap between the Axiom and the Watkins Collection.</td></tr><tr><td colspan="2"><strong>Workaround: </strong>There is currently no workaround.</td></tr></tbody></table></figure> </div> </article> </div> <footer class="site-info" itemscope itemtype="http://schema.org/WPFooter"> <a href="http://wordpress.org/" title="Semantic Personal Publishing Platform">Proudly powered by WordPress</a>. 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