Hi Claude, >From my previous experience working on Ensembl rember that occassionally martdb and ftp would get out of sync. Perhaps this is what happened this time?
I am forwarding your email to the users mailing list. Rhoda or someone else from Ensembl should be able to comment on this. a On Tue, Sep 20, 2011 at 12:00 PM, Claude Chelala <[email protected]>wrote: > > ------ Forwarded Message > *From: *Claude Chelala <[email protected]> > *Date: *Tue, 20 Sep 2011 16:55:36 +0100 > *To: *Arek Kasprzyk <[email protected]> > *Cc: *Dayem Ullah <[email protected]> > *Conversation: *Ensembl mart tables - corrupted? > *Subject: *Ensembl mart tables - corrupted? > > Dear Arek > > Dayem (cc’d on this email) joined my group recently and is in charge of > updating SNPnexus software preparing for a new release. He is experiencing > few problems when working with ensembl_mart_63 (and 64) tables and would > appreciate your help to sort this out. > > When working on biomart release 63, he observed the following discrepancy > between Public MySQL Server martdb.ensembl.org and the corresponding > downloadable version (Pub Mysql tables as in ensembl release from > ftp://ftp.ensembl.org/pub/release-63/mysql/ensembl_mart_63). > > ftp://ftp.ensembl.org/pub/release-63/mysql/ensembl_mart_63 > Database name: ensembl_mart_63 > Table name: hsapiens_gene_ensembl__exon_transcript__dm > > It appears that exons are not mapped properly with the corresponding > transcripts from hsapiens_gene_ensembl__transcript__main table. The mapping > at martdb.ensembl.org tables seems to be correct. > > The exon information with respect to exon_id (*exon_id_1017*) are mostly > different in two versions. With respect to exon name (*stable_id_1016*), > the other information appears to be same in two versions except the > corresponding mapping with transcript (*transcript_id_1064_key*). > > The example is shown in the file attached. For transcript ENST00000302036 > (*transcript_id_1064_key=*342178) the pub release version mapping to > corresponding exons is incorrect, whereas public server martdb.ensembl.org > version > gives correct mapping. Subsequently, we can see that the same exon id refers > to different exons or same exon maps to different transcript. > > We suspect that the ensembl Mysql release version of the table > hsapiens_gene_ensembl__exon_transcript__dm > is corrupted and martdb.ensembl.org table is correct. > However, we noted another point: the number of rows in the tables are > different as well: > > martdb.ensembl.org > Database name: ensembl_mart_63 > Table name: hsapiens_gene_ensembl__exon_transcript__dm > 1161741 rows > > ftp://ftp.ensembl.org/pub/release-63/mysql/ensembl_mart_63 > Database name: ensembl_mart_63 > Table name: hsapiens_gene_ensembl__exon_transcript__dm > 1178393 rows > > Could you please help us to get the correct mappings and tables? > > Thank you > > Regards > Claude > ------ End of Forwarded Message > > > > > > > > > > This email may contain information that is privileged, confidential or > otherwise protected from disclosure. > It must not be used by, or its contents copied or disclosed to, persons > other than the addressee. > If you have received this email in error please notify the sender > immediately and delete the email. > This message has been scanned for viruses. > >
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