On 18 Sep 2006, at 10:14, Steve Taylor wrote:
Hi,
apologies for the delay in answering - it slipped through the net
yesterday. Unfortunately the EBI spam monitor removed the attachments
so can you send me the mail again with the error message pasted in
the text. Also which version of MartEditor - the latest stable 0_4
branch one downloaded from biomart.org presumably?
Unfortunately I can't cut and paste the error message from the window
(would be nice to be able to do this in biomart 0.5 :-)).
I guess I will have to type it! When exporting I got the message:
The following names are incorrect links
hsapiens_gene_ensembl_structure__str_chrom_name in exportable gtf
hsapiens_gene_ensembl_structure__exon_chrom_start in exportable gtf
hsapiens_gene_ensembl_structure__exon_chrom_end in exportable gtf
hsapiens_gene_ensembl_structure__transcript_chrom_strand in exportable
gtf
hsapiens_gene_ensembl_structure__gtf_cds_chrom_start in exportable gtf
hsapiens_gene_ensembl_structure__gtf_cds_chrom_end in exportable gtf
hsapiens_gene_ensembl_structure__gtf_start_codon_start in exportable
gtf
hsapiens_gene_ensembl_structure__gtf_stop_codon_start in exportable gtf
hsapiens_gene_ensembl_structure__gtf_frame in exportable gtf
hsapiens_gene_ensembl_structure__gene_stable_id in exportable gtf
hsapiens_gene_ensembl_structure__gene_stable_id_v in exportable gtf
hsapiens_gene_ensembl_structure__transcript_stable_id_v in exportable
gtf
hsapiens_gene_ensembl_structure__exon_stable_id_v in exportable gtf
MartEditor is the version downloaded from
http://www.biomart.org/MartJ1.html
Kind Regards and Thanks,
Steve
Hi Steve,
sorry for the late reply. Please remove exportable 'gtf' from this
dataset
and then export it. It should work fine.
apologies for this oversight
a.
Best wishes
Damian
On Wed, 13 Sep 2006, Steve Taylor wrote:
Hi,
I am trying to adapt the BioMart ensembl_mart_40 database to add
sage tag data. To start, I thought I would add a new table based on
one of the xref tables. My table
(hsapiens_gene_ensembl__xref_sage_tag__dm) I have added is very
similar to other xref tables (contains columns gene_id_key,
gene_stable_id, transcript_id_key,
transcript_stable_id,translation_id, translation_stable_id,
display_id_list, dbprimary_id). After importing
ensembl_mart_40.hsapiens_gene_ensembl in MartEditor I edited it
(see attached snaphot of MartEditor sshot-2.png) but when I try and
export I get the error message (see sshot-1.png).
I have also saved the xml from the hsapiens_gene_ensembl at:
http://neelix.molbiol.ox.ac.uk:8080/userweb/staylor/biomart/
ensembl_mart_40.hsapiens_gene_ensembl.xml
I am obviously missing a further configuration step but I am unsure
what to do next.
Thanks for any help,
Steve
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Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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