Hello Anita, It is possible to check your positions against a reference SNP database to see if there is overlap. This will link any known SNPs rs numbers. The recommended tools would be in "Operate on Genomic Intervals". Join would be a basic choice, but other Tools that merge/cluster the data may be of interest. To start, load your dataset and a dbSNP dataset. It would be quickest to load from "Shared Data -> Data Library" using the data in “Putative SNP phenotypes -> dbSNP130.txt". The dataset is sourced from hg18 dbSNP130. Please use the option "View information" (click on arrow next to data set name) to understand the contents and formatting. The idea would be to format your data also into Interval format, then Join. From a quick look at your sample, the chromosome names would have to be modified (add in "chr"), column 2 reduced in value by "1", and column 3 removed. Tools in "Text Manipulation" can help to do these tasks. Good luck with your project and please let us know if you need more help, Jen Galaxy team On 11/10/10 1:51 PM, Lakatos, Anita wrote:
Polymorphic variations were retrieved from a sequenced data (aligned to hg18). The output file contains the chr and the position but no (rs number). The tab delimited file with map extension is
Chr pos # pos
1 82496 0 82496
1 91549 0 91549
1 98173 0 98173
1 696970 0 696970
Could you please let me know if there is way with galaxy to retrieve the rs number for these SNPs? I am open to any solution!
Many thanks for your help,
Anita Lakatos
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