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Hello Will,<br>
<br>
Ok that makes perfect sense.<br>
Thank you for help as always Will.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">El 15/09/14 a las #4, Will McLaren
escribió:<br>
</div>
<blockquote
cite="mid:CAMVEDX0JnkLqJHBFhjrS9BE2cqDacncQQtU1gnVzWCGa=LGAPQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>It seems we haven't made available on our FTP site the
dumps for *_76_37.</div>
<div><br>
</div>
<div>The data is in fact identical to *_75_37 so you've a couple
of solutions:</div>
<div><br>
</div>
<div>1) Point VEP to the 75 database (--db_version) and the 76
cache (--cache_version)</div>
<div><br>
</div>
<div>2) Create *_76_37 databases with the *_75_37 data and patch
the schemas to 76 using ensembl/misc-scripts/<a
moz-do-not-send="true" href="http://schema_patcher.pl">schema_patcher.pl</a></div>
<div><br>
</div>
<div>Regards</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 15 September 2014 14:26, Guillermo
Marco Puche <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066"> Hello Will,<br>
<br>
Indeed I run a local Ensembl installation. I've installed
homo_sapiens_*_76_38 that's why I'm getting the error. It
was a missunderstading from my part. I guess it's time to
move to GRCh38.<br>
Anyways I was trying to find homo_sapiens_*_76_37 MySQL
links for download but I just find homo_sapiens_*_76_38 on
FTP server.<br>
<br>
Could you give me a link to a mirror for
homo_sapiens_*_76_37?<span class=""><br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
</span>
<div>El 15/09/14 a las #4, Will McLaren escribió:<br>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>Are you also running your own database
server?</div>
<div><br>
</div>
<div>The GRCh37 v76 databases are hosted on a
different port on <a moz-do-not-send="true"
href="http://ensembldb.ensembl.org"
target="_blank">ensembldb.ensembl.org</a>
(3337); to get the VEP to use this you can add
the flag --port 3337 to your command line. If
you don't use the DB (most VEP functionality
does not use the DB at all, see <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations"
target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations</a>),
you can bypass this completely and use
--offline. See <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly"
target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly</a>
for more details.</div>
<div><br>
</div>
<div>If you are using your own DB server then you
will need to make sure you have mirrored the
correct human databases; you should have
homo_sapiens_*_76_37 (* being core, variation
and funcgen).</div>
<div><br>
</div>
<div>HTH</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 15 September 2014
09:04, Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066"> I
forgot to mention than I've already tried to
specify assembly with VEP "--assembly" flag:<br>
<br>
ERROR: Assembly version specified by
--assembly (GRCh37) and assembly.default
meta key (GRCh38) do not match<br>
<br>
<div>El 15/09/14 a las #4, Guillermo Marco
Puche escribió:<br>
</div>
<blockquote type="cite">
<div>
<div> Hello,<br>
<br>
I installed Ensembl 76 on my local
server. I'm not ready yet to annotate
variants vs GRCh38.<br>
I thought that ensembl 76 version
supports both GRCh37 and GRCh38. I
downloaded 76 vep cache for GRCh37:<br>
<br>
<a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-76/variation/VEP/homo_sapiens_merged_vep_76_GRCh37.tar.gz"
target="_blank">ftp://ftp.ensembl.org/pub/release-76/variation/VEP/homo_sapiens_merged_vep_76_GRCh37.tar.gz</a><br>
<br>
I get the following error:<br>
<br>
<b>ERROR: Cache assembly version
(GRCh37) and database or selected
assembly version (GRCh38) do not
match.</b><b><br>
</b><br>
I got a bit confused since I saw both
cache for GRCh37/38, I would like to
know if in Ensembl 76 I can stilll
annotate with GRCh37 or I just have to
move asap to GRCh38 to use 76 version.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
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