<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span class="">Hi Duarte,<br class=""></span><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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" class="">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 class=""><span style="color: rgb(23, 43, 77); orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="color: rgb(23, 43, 77); orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class="">As for release 99, the GRCh37 RefSeq cache contains 2 different RefSeq versions</span></div><div class=""><ul style="margin: 10px 0px 0px; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class=""><li style="color: rgb(23, 43, 77);" class="">the last annotation on GRCh37 </li><ul class=""><li class=""><font color="#172b4d" class=""><span style="caret-color: rgb(23, 43, 77);" class=""><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" class="">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 class=""><font color="#172b4d" class="">a GRCh38 annotation projected to GRCh37</font><br class=""></li><ul style="margin: 0px; list-style-type: disc;" class=""><li class=""><font color="#172b4d" class=""><span style="caret-color: rgb(23, 43, 77);" class=""><a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.109/GRCh37.p13_interim_annotation/" class="">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 style="orphans: 2; widows: 2;" class=""><br class=""></div><div style="orphans: 2; widows: 2;" class=""><br class=""></div><div style="orphans: 2; widows: 2;" class=""><font color="#172b4d" class="">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" class="">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 style="orphans: 2; widows: 2;" class=""><br class=""></div><div style="orphans: 2; widows: 2;" class="">Kind Regards,</div><div style="orphans: 2; widows: 2;" class="">Andrew</div><div class=""><br class=""></div></div><div class=""><br class=""></div><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 16 Apr 2020, at 17:01, Duarte Molha <<a href="mailto:duartemolha@gmail.com" class="">duartemolha@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Dear Devs</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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;" class=""><br class=""></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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)" class="">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;" class=""><br class=""></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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;" class=""><br class=""></div><br class=""><b class="">2019-06-28<br class="">(GCF_000001405.39_GRCh38.p13_genomic.gff)</b><table class="gmail-ss" 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 class=""><tr style="vertical-align:top" class=""></tr></tbody></table><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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;" class=""><br class=""></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">You have simply listed it as :</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""></div><b class="">2015-01</b><div class=""><b class=""><br class=""></b>And I have not been able to match this date to any of the GCF files <div class=""><br class=""></div><div class="">The latest I could find for GRCh37 is </div><div class=""><br class=""></div><div class=""><a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/" class="">https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/</a> </div><div class=""><br class=""></div><div class="">but this file dates to
<span style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px;" class="">2013/06/28</span> </div><div class=""><br class=""></div><div class="">Can you please point me where I can get the 2015-01 refseq GFF source file you have used for the cache?</div><div class=""><br class=""></div><div class="">Best regards</div><div class=""><br class=""></div><div class="">Duarte<br class=""></div><div class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""></div></div></div></div></div></div></div>
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