On 2 Jan 2007, at 17:30, Charles Danko wrote:
Hi,
I've noticed that certain genes are missing from BioMart Results when
using the web interface.
To replicate the problem:
Select Dataset ENSEMBL 42 GENE (SANGER)
Species: Rattus norvegicus genes (RGSC3.4)
Under attributes select Sequences.
Sequences, select: Flank-coding region (Transcript) or Peptide or
Coding Sequence
Upstream flank: 2000 (selected)
Gene Attributes: ENSEMBL Gene ID
Filters:
Select ID list limit, paste in Gene ID: ENSRNOG00000000065
Select Count: shows 1 / 27,249 Genes
Select Results ... blank, no results!!!!!!
Searching for ENSRNOG00000000065 under ENSEMBL gives a gene with 1
transcript that should come up under biomart?!
Other genes work just fine (e.g. ENSRNOG00000005947). Other genes
work only when selecting either Flank-coding region (Transcript) or
Peptide or Coding Sequence but not all 3.
Hi Charles,
What am I doing wrong?
nothing :-) but thanks for helping us to find a bug that has proved to
be very elusive.
The gene is actually present if you select any other (apart from
sequence) attributes
but somehow when you select sequence it does not come up.
Please bare with us while we are investigating further to get to the
bottom of it.
We'll get back to you when it is fixed
a.
Thanks very much!
Charles Danko
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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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