Hello, I am currently working with BioMart to try to export SNP identifiers in the Mouse organism based on a chromosomal region (a gene start and end position). These are the only filters chosen on the filters pane. In the Attributes pane I have chosen to export the RefSnp Id, the strain name, the strain allele, the Ensembl stable gene Id, the chromosome, the chromosomal position of the SNP, the Ensembl gene location (coding etc), and validation.
However, when I obtain the results of SNPs for the gene GPX2, (start position = 77,711,490; end position = 77,714,215), I only obtain 2 different RefSnp Ids, compared to the 12 RefSnp Ids found in dbSNP at the NCBI website. After I investigated the cause of this I found that the Strain attribute in BioMart was acting as a filter and not a display option, where any SNPs with no strain information would not be included in the output. Could you please tell me if this is intentional, and if so the reason. many thanks, Paul Fisher
