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Biomart Snp Download Problem.

Can anyone download this [http://i.imgur.com/ompc0.png] file in its entirety ? I cant seem to get it and the URL does not work--

Related: http://biostar.stackexchange.com/questions/2356/problem-with-dbsnp-sequence-variation-download-using-biomart

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No surprise that the URL does not work. It does not look like an externally-accessible server and it contains a session key specific to the user and time of access. You need to recreate the BioMart query in a fresh session at a recognized server and try again.

closed as no longer relevant, because 1. the URL is not supposed to work that way, and 2. the problem or impossibility of downloading all SNPs from biomart has been covered in the related question.

It was not possible to obtain large numbers of mouse SNPs from the biomart web interface, If you need large numbers of SNPs you must use the API.

For my case where I wanted the names and locations of SNPs variant between two mouse strains. you can query the biomart API as per the biomart documentation.

This is useful for example if you are trying to find probes on a microarray that maybe be SNP affected between two mouse strains.

This was accomplished "c57bl10j" and "nodltj" (chromosome 1): wget -O resultsnod1.txt 'http://www.biomart.org/biomart/martservice?query=<Query virtualSchemaName="default" formatter="DIFF_TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" &gt;<Dataset="" name="mmusculus_snp" interface="default" &gt;<Filter="" name="chr_name" value="1"/><Attribute name="refsnp_id"/><Attribute name="chr_name"/><Attribute name="chrom_start"/><Attribute name="c57bl_10j"/><Attribute name="nod_ltj"/></Dataset></Query>'

1 answer

Related: - Problem With Dbsnp Sequence Variation Download Using Biomart

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