This is more likely to be a problem with the count button (usually when people report problems with it it reports less than what you get, not more...), or a change in the internal structure of the dbSNP database since your previous attempt. Do you remember what release of Ensembl your previous attempt was made with? Then we can compare the two in the archives to see if we can spot any differences in the data.
cheers, Richard On Wed, February 7, 2007 10:00 pm, Amir Karger wrote: >> From: Arek Kasprzyk [mailto:[EMAIL PROTECTED] >> >> On 7 Feb 2007, at 21:09, Amir Karger wrote: >> >> > I'm downloading all valid dbSNPs from Biomart.org. I >> selected ensembl >> > variation 42, selected the "valid only" restriction, and left the >> > default attributes. >> > >> > When I ask for a count, there are 5.6M, which is about what >> I got a few >> > months ago when I downloaded a slightly different version >> from ensembl. >> > However, when I do the actual download, I get only 1.9M lines. I >> > downloaded as tsv as well as xml. >> > >> > -Amir Karger >> > >> >> >> Amir, >> can you try 'notify by email' option when downloading a file >> and check if the problem still persists? > > I used the notify by email mechanism for both. I've been finding that > more reliable than the regular download. I'll mention that I downloaded > a gz, which successfully unzipped, so I don't think it's a problem in > transmission. > > -Amir > >> >> >> a. >> >> >> >> -------------------------------------------------------------- >> ---------- >> ------- >> 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 >> -------------------------------------------------------------- >> ---------- >> ------- >> >> >> >> > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK
