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Background image by Spencer Phillips</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-12384" class="post-12384 page type-page status-publish hentry"> <header class="entry-header"> <h1 class="entry-title" itemprop="name">Ensembl 100</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>Truncated GVF and VCF files for some non-vertebrate species</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 100, Ensembl 101</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>The GVF and VCF files that we make available on the FTP site, which store variation data, were inadvertently truncated for all fungi, metazoa, and protist species. This affects Ensembl Genomes releases 47 and 48.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>The affected GVF and VCF files have been fixed and are now available in the respective FTP directories.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Missing RefSeq data in homo_sapiens otherfeatures 100</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 100, Ensembl 101, Ensembl 102</td> </tr> <tr> <td colspan="2"><strong>Description:</strong>There are a number of RefSeq genes missing in the homo_sapiens_otherfeatures_100_38 database.</p> <p>This will also affect VEP queries using the RefSeq transcript set.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>The Ensembl transcript set is unaffected, but there is no work-around for VEP queries using the RefSeq or merged transcript set.</p> <p>This will be fixed in Ensembl 103.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Missing Goldfish JSON file</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>The JSON file for the Goldfish (<em>Carassius auratus</em>) is not available on the Ensembl ftp site.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>The data that would have been in the JSON file is available in a range of <a class="external-link" href="http://www.ensembl.org/info/data/ftp/index.html" rel="nofollow">other files</a>.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Incomplete mapping in Assembly Converter</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Mirrors</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 98, Ensembl 99, Ensembl 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>The following species have no mappings between new and old assemblies.<br /> This means that the Assembly Converter tool will not present these, even though such mappings are possible.</p> <p>Fungi: Saccharomyces cerevisiae (EF1 and R64-1-1)</p> <p>Protists: Thalassiosira pseudonana (ASM14940v1_bd and ASM14940v2)</td> </tr> <tr> <td colspan="2"><strong>Workaround:</strong></p> <p><span style="font-size: inherit; font-family: inherit;">No workaround.</span></td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Inconsistencies between core and core-like dbs</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Mirrors</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>The assembly name and accession do not match between the human rnaseq (GRCh38.p10, GCA_000001405.25), otherfeatures (GRCh38.p12, GCA_000001405.27) and core (GRCh38.p13, GCA_000001405.28) databases. The otherfeatures database has the expected GRCh38.p10 assembly and seq_region tables though.</p> <p>The assembly name and accession do not match between the mouse rnaseq (GRCm38.p5, GCA_000001635.7) and core (GRCm38.p6, GCA_000001635.8) databases. The rnaseq database has the expected GRCm38.p6 assembly and seq_region tables though.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>No workaround.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Erroneous transcript (ENSRNASEQT00001237576) in Pig RNAseq data</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Archives</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 99, Ensembl 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>There is a transcript in the Pig reference rnaseq database with no exons, and no translation. We will remove this transcript and hand over the corrected rnaseq database.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>No workaround.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Links to RefSeq genes do not work</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Mirrors</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 99, Ensembl 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Links to RefSeq genes in region views do not work, because they use an internal identifier rather than the gene ID.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Links to transcripts are correct, so these can be used to navigate to the correct page on the NCBI website.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Drosophila melanogaster RNA gene cross-reference links do not work</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Mirrors</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 99, Ensembl 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Rfam and miRBase cross-reference links do not work, because they use the FlyBase ID instead of the RNA gene.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Search for the Rfam or miRBase ID on the respective website.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Gene name cross-reference links do not work</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site, Mirrors</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 99, Ensembl 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Cross-reference links to HGNC, MGI, and ZFIN do not link to the correct page, because they use the name rather than the numeric identifier.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Search for the gene name on the HGNC, MGI, or ZFIN website.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Remove semicolons [;] from gene names in dumped GTF 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 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>The Arabidopsis thaliana GTF file available for download contains semicolons in the gene_name within the attributes. This is a disallowed character for many downstream programmes (for example htseq-count).</p> <p>This does not affect the GFF version of the same file.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>Escape forbidden GTF characters, such as semicolons, within attributes.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Gene trees missing human ncRNA genes</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 99, Ensembl 100</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Due to missing Rfam references, a number of human ncRNA genes have not been clustered correctly and are therefore missing from gene trees and homology predictions.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>No workaround. Use Ensembl 98 if possible.</td> </tr> </tbody> </table> <table class="table table-bordered"> <tbody> <tr> <td colspan="2"> <h3>Drosophilidae cores imported from FlyBase have stop codon missing from their CDSs</h3> </td> </tr> <tr> <td class="col-md-2"><strong>Affects: </strong>Live site</td> <td class="col-md-4"><strong>Versions: </strong>Ensembl 98, Ensembl 99, Ensembl 100, Ensembl 101</td> </tr> <tr> <td colspan="2"><strong>Description: </strong>Drosophilidae cores imported from FlyBase have missing stop codon in their CDS. No proteins and their domains are affected.</td> </tr> <tr> <td colspan="2"><strong>Workaround: </strong>No workaround. The species core will be reimported from FlyBase in a future release.</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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