Hi Claude
I will look into this issue and get back to you as soon as possible.
Regards
Rhoda
On 21 Sep 2011, at 13:58, Arek Kasprzyk wrote:
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
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_______________________________________________
Users mailing list
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https://lists.biomart.org/mailman/listinfo/users
Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
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