<div dir="ltr">Many thanks<div><br></div><div>Good to know that going forward there will be a single source file.</div><div><br></div><div>Unfortunately right now we are using version 98 and will not be transitioning in the short term. </div><div><br></div><div>Could you let me know the source ref files for version 98 cache?</div><div>Are they the same as version 99 you listed?</div><div><br></div><div>Many thanks again</div><div><br></div><div>Duarte</div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 17 Apr 2020 at 17:42, Andrew Parton <<a href="mailto:aparton@ebi.ac.uk">aparton@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;"><span>Hi Duarte,<br></span><div><br></div><div>Unfortunately we don’t have one GFF file that covers all transcripts within our GRCh37 cache files. Additionally, we will be providing significant updates to these files very soon.</div><div><br></div><div>For release 100, scheduled for release at the end of April, a new set of RefSeq transcripts are included within our GRCh37 cache files. They can be found here: <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz</a></div><div><span style="color:rgb(23,43,77);background-color:rgb(255,255,255)"><br></span></div><div><span style="color:rgb(23,43,77);background-color:rgb(255,255,255)">As for release 99, the GRCh37 RefSeq cache contains 2 different RefSeq versions</span></div><div><ul style="margin:10px 0px 0px;font-variant-ligatures:normal;background-color:rgb(255,255,255)"><li style="color:rgb(23,43,77)">the last annotation on GRCh37 </li><ul><li><font color="#172b4d"><span><a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz</a></span></font></li></ul><li><font color="#172b4d">a GRCh38 annotation projected to GRCh37</font><br></li><ul style="margin:0px;list-style-type:disc"><li><font color="#172b4d"><span><a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.109/GRCh37.p13_interim_annotation/" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.109/GRCh37.p13_interim_annotation/</a></span></font></li></ul></ul><div><br></div><div><br></div><div><font color="#172b4d">If you would like to have a closer look at the exact data included within the RefSeq cache file, you can access our publicly available mysql database by following these instructions: </font><a href="https://www.ensembl.org/info/data/mysql.html" target="_blank">https://www.ensembl.org/info/data/mysql.html</a> - the homo_sapiens_otherfeatures_99_37 database contains the transcript sets included within our cache files.</div><div><br></div><div>Kind Regards,</div><div>Andrew</div><div><br></div></div><div><br></div><br><div><br><blockquote type="cite"><div>On 16 Apr 2020, at 17:01, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Dear Devs</div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><br></div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">I was wondering if you could help me with the source of the cache data for VEP</div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><br></div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">ON this link <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html" style="font-family:Arial,Helvetica,sans-serif;font-size:small;color:rgb(5,99,193)" target="_blank">https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html</a></div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><br></div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">you list the refseq source of the transcripts used to this file:</div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><br></div><br><b>2019-06-28<br>(GCF_000001405.39_GRCh38.p13_genomic.gff)</b><table style="width:auto;border:1px solid rgb(204,204,204);margin:0px 0px 16px;border-spacing:0px;color:rgb(102,102,102);font-family:"Luxi Sans",Helvetica,Arial,Geneva,sans-serif;font-size:12.8px"><tbody><tr style="vertical-align:top"></tr></tbody></table><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">This is great but I am interested in also getting the correct source for the hg19 version</div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><br></div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">You have simply listed it as :</div><div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><br></div><b>2015-01</b><div><b><br></b>And I have not been able to match this date to any of the GCF files <div><br></div><div>The latest I could find for GRCh37 is </div><div><br></div><div><a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/" target="_blank">https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/</a> </div><div><br></div><div>but this file dates to  

<span style="font-family:arial,helvetica,clean,sans-serif;font-size:13px">2013/06/28</span> </div><div><br></div><div>Can you please point me where I can get the 2015-01 refseq GFF source file you have used for the cache?</div><div><br></div><div>Best regards</div><div><br></div><div>Duarte<br></div><div><div><div dir="ltr"><div dir="ltr"><div></div></div></div></div></div></div></div>
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