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All rights reserved. Background image by Spencer Phillips</div> </aside> <aside id="eu_cookie_law_widget-2" class="widget widget_eu_cookie_law_widget"> <div class="hide-on-button" data-hide-timeout="30" data-consent-expiration="365" id="eu-cookie-law" > <form method="post"> <input type="submit" value="Close and accept" class="accept" /> </form> This website requires cookies, and the limited processing of your personal data in order to function. 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-13632" class="post-13632 page type-page status-publish hentry"> <header class="entry-header"> <h1 class="entry-title" itemprop="name">Ensembl 105</h1> </header> <div class="entry-content" itemprop="articleBody"> <table class="table table-bordered"> <thead class="thead-light"> <tr> <th colspan="2">Known bugs in Ensembl</th> </tr> </thead> <tbody id="known_bugs_table"> <tr> <td colspan="2"> <h3>Comparative data display issues</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Expected Versions: </strong>Ensembl 103, 104, 105</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Some of the available comparative genomics data is not currently displayed on the live site. This affects all vertebrate and non vertebrate species across Ensembl, Ensembl Genomes and Pan-Compara. Identified issues include:</p> <ul> <li>Known homologues missing from homologue tables</li> <li>Incorrect summary statistics in the orthologue summary table reporting homology types across taxa</li> <li>Missing species list without orthologues</li> <li>Unavailable gene tree links on the gene tab</li> </ul> </td> </tr> <tr> <td colspan="2"><strong><strong>Workaround: </strong></strong>This will be fixed in an upcoming Ensembl release, in the meantime the full data can be accessed via <a href="https://www.ensembl.org/biomart/martview">BioMart</a> or the <a href="https://www.ensembl.org/info/data/ftp/index.html">FTP</a> site. Alternatively, you can use previous Ensembl releases available in our <a href="https://www.ensembl.org/info/website/archives/index.html">archives</a>.</td> </tr> <tr> <td colspan="2"> <h3>Missing Whole Genome Alignment Coverage scores</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Expected Versions: </strong>Ensembl 103, 104, 105</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>WGA Coverage scores might be missing (equal 0.00) for certain high quality homologues.</td> </tr> <tr> <td colspan="2"><strong><strong>Workaround: </strong></strong>This will be fixed in an upcoming Ensembl release, in the meantime you can use previous Ensembl releases available in our <a href="https://www.ensembl.org/info/website/archives/index.html">archives</a>.</td> </tr> <tr> <td colspan="2"> <h3>Inconsistency in transcripts numbering in GFF3 and GTF exported files</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 102, 103, 104, 105</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>We noticed, from a bug report that some inconstencies may appear in particular cases between our GFF3 and GTF FTP files available.</p> <p>Sometime, depending on data underlying our dumps, the number of transcripts retrieved may differ from one file to the other, for the same species.</p> <p>The main difference between GTF and GFF3 dumping is that for GTF, we get the transcripts from the gene ($gene->get_all_Transcripts) while for the GFF3, we get the transcripts from the underlying slice ($transcript_adaptor->fetch_all_by_Slice)</p> <p>https://github.com/Ensembl/ensembl-production/blob/release/104/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm#L199<br /> https://github.com/Ensembl/ensembl-io/blob/release/104/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm#L112</p> <p>This means if the transcript goes over the boundaries of the slice, we might not dump it although we dump the genes.<br /> This currently only happens with genes on patches, where some transcripts can be entirely outside of the patch region due to the fact that we create a fake chromosome including the patch.<br /> In the future, we are planning to store the patches as standalone scaffolds, and those transcripts will be removed entirely, hence not being included in either the GTF or GFF3 dumps</p> <p>We plan to fix this from 106 onwards.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>No work around. Except using most up to date datasets</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>1000 Genomes minor allele frequency incorrect for duplications</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Staging, GRCh37</td> <td class="col-md-4"><strong>Expected Versions: </strong>Ensembl 103, 104, 105</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Some insertion/deletion variants which can be described as duplications currently have incorrect global allele frequencies from the 1000 Genomes Project reported in the Ensembl variant and transcript views, BioMart and in Ensembl VEP. Versions 103 – 104 are affected. The continental population frequencies for these variants are correct and the problem can be identified by comparing the two. Example: rs199588481 where an ‘A’ is inserted adjacent to an ‘A’ , the VCF reference allele ‘A’ is annotated as the minor allele, when the alternate allele ‘AA’ should be. This issue will be resolved in Ensembl VEP version 105, which will be released in the autumn. BioMart and the Ensembl browsers will be fixed for version 106.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>We advise ignoring these global frequencies and filtering using the continental frequencies instead.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>COSMIC data not present in Ensembl 105 GRCh38 browser views or BioMart</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Expected Versions: </strong>Ensembl 105</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Somatic mutations from the COSMIC project will not be displayed in browser views, available for querying in BioMart, or available via our APIs for assembly GRCh38 in Ensembl version 105. These data will return in Ensembl version 106.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>The Ensembl version 104 archive site and REST archive service can be used to view/access COSMIC data</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3><em>Corylus avellana</em> left out of Compara</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Expected Versions: </strong>Ensembl 105, 106</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Because of a typo <em>Corylus avellana</em> has been left out of the compara gene tree in 105, it will be added back in 106.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>There is currently no workaround for this.</td> </tr> </tbody> </table> <table class="table table-bordered" style="height: 5px;" width="913"> <tbody> <tr> <td colspan="2"> <h3>Missing MT ‘sequence_location’ attribute</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Expected Versions: </strong>Ensembl 105, 106</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Mitochondrial DNA sequences from 12 species (see list of species below) were mistakenly processed as nuclear DNA sequences which then affected pairwise and multiple genome alignments, and consequently syntenies for vertebrate and metazoan genomes involved.<em> Anolis carolinensis</em><br /> <em>Ficedula albicollis</em><br /> <em>Macaca fascicularis</em><br /> <em>Mastacembelus armatus</em><br /> <em>Meleagris gallopavo</em><br /> <em>Papio anubis</em><br /> <em>Pongo abelii</em><br /> <em>Rattus norvegicus</em><br /> <em>Scophthalmus maximus</em><br /> <em>Anopheles coluzzii ngousso</em><br /> <em>Nannizzia gypsea cbs 118893</em><br /> <em>Ustilago bromivora</em></td> </tr> <tr> <td colspan="2"><strong>Workaround:</strong>There is currently no workaround for this.</td> </tr> </tbody> </table> <table class="table table-bordered" style="height: 5px;" width="913"> <tbody> <tr> <td colspan="2"> <h3>Missing Rat microarray data</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Expected Versions: </strong>Ensembl 105, 106</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>The Rat assembly was updated in Ensembl Release 105 to mRatBN7.2, but microarray probeset information (oligo probes) was not updated. This means that microarray and oligo probe mapping is missing from Release 105 in the genome browser and BioMart.</td> </tr> <tr> <td colspan="2"><strong><strong>Workaround: </strong></strong>Microarray and oligo probe information for the previous assembly (Rnor_6.0) can be accessed using the archive sites or the 104 release of BioMart (http://may2021.archive.ensembl.org/index.html).</td> </tr> </tbody> </table> </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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