On 4 Aug 2006, at 19:27, Bromberg, Susan wrote:
Bert,
Hi Susan,
I think I have found the source of my problems. If I use no filters
and
then request strain and strain allele in the output, I get only ~7000
rows back, and every row has the strain information. If I leave out
the
strain information, I get as many as 87,000 rows depending on what
fields I have returned. It seems that the strain section in the output
form is actually filtering the results. Is this correct?
unfortunately yes. It was brought to our attention just a couple of days
ago that the strain table contains only snp with strain info therefore
joining this table
with the main dataset limits it to snp with strain info only (you
correctly describe
it as behaving as filter). We'll look into rectifying this situation in
the near future,
Unfortunately it is too late to correct for the about to be released
ensembl 40.
a.
I am also copying this to the mart_dev email, which I was just alerted
to.
Thanks for you help.
Susan
Susan K. Bromberg, Ph.D.
Bioinformatics Program (http://www.brc.mcw.edu)
Human Molecular and Genetics Center (http://hmgc.mcw.edu)
Medical College of Wisconsin
8701 Watertown Plank Rd.
Milwaukee, WI 53226
414-456-7515
[EMAIL PROTECTED]
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Friday, August 04, 2006 7:14 AM
To: Bromberg, Susan
Subject: Re: BioMart: Susan Bromberg [EnsHelp:2006214.84581]
Hello Susan,
It works for us. However, exporting in Excel resulted in
Excel program failure (I guess because of the large number of
rows), but exporting it in text format and then opening it in
Excel worked fine. If a SNP is displayed multiple times this
is because it maps to multiple genes and/or transcripts. You
can verify this by also exporting the Ensembl Gene and Transcript ID.
I hope this answers your question. Please let us know if you
have any other questions or problems.
With kind regards,
Bert Overduin
(Ensembl Helpdesk)
0
Your original request, received: 2006-08-03 23:29:41
Referrer: http://www.ensembl.org/Rattus_norvegicus/helpview
I am trying to download all rat SNPs using Biomart. I
select the SNP
dataset for rat and no filters. It says there are 37500 entries.
However I get back only ~ 1700 rows and these include many
duplicates.
How can I get all 37500 SNPs back?
Thank you.
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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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