Bert, 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?
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. > >
