<div dir="ltr"><div>Hi all,<br><br>Couple of doubts:<br><br><ol><li>Is it possible to use local version of Variation Database and use online version of core database from perl API's?</li></ol><br>I am trying to get all LD pairs for given set snps.  (Script Attached: <a href="http://ld.pl">ld.pl</a>). I am getting following error:<br>
<br><br></div>-------------------- WARNING ----------------------<br>MSG: Could not find Slice adaptor in the registry for Homo_sapiens variation<br><br>FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 899<br>CALLED BY: Variation/DBSQL/VariationFeatureAdaptor.pm  LINE: 738<br>
Ensembl API version = 63<br>---------------------------------------------------<br><br>-------------------- EXCEPTION --------------------<br>MSG: Could not get adaptor Slice for Homo_sapiens variation<br><br>STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /home/gaurav/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:904<br>
STACK Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::_objs_from_sth /home/gaurav/ensembl-variation/modules//Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:738<br>STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch /home/gaurav/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:528<br>
STACK Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Variation /home/gaurav/ensembl-variation/modules//Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:280<br>STACK toplevel <a href="http://ld.pl:51">ld.pl:51</a><br>
Ensembl API version = 63<br>---------------------------------------------------<br><br><div>Please help to resolve above issue. I have also created a registry file containing all configuration parameters. (attached ensembl_registry.conf)<br>
<br>While downloading mysql dump of human variation database from ftp site. There is no table corresponding to mart_transcript_variation.txt.gz in sql file. Can you please let me know, what this file is used for?<br><br>-- <br>
Regards<br><br>Gaurav Thareja<br>
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