Re: [BioMart Users] FW: Ensembl mart tables - corrupted?

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Re: [BioMart Users] FW: Ensembl mart tables - corrupted?

Arek Kasprzyk
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 <[hidden email]> wrote:

------ Forwarded Message
From: Claude Chelala <c.chelala@...>
Date: Tue, 20 Sep 2011 16:55:36 +0100
To: Arek Kasprzyk <Arek.Kasprzyk@...>
Cc: Dayem Ullah <d.ullah@...>
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

 

 

 

 

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Re: [BioMart Users] FW: Ensembl mart tables - corrupted?

Rhoda Kinsella
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 <[hidden email]> wrote:

------ Forwarded Message
From: Claude Chelala <c.chelala@...>
Date: Tue, 20 Sep 2011 16:55:36 +0100
To: Arek Kasprzyk <Arek.Kasprzyk@...>
Cc: Dayem Ullah <d.ullah@...>
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.


_______________________________________________
Users mailing list
[hidden email]
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.


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users