Hi Prithvi, I am sorry for the delayed response. Do you have the identifiers for the 200,000 SNPs (rs####)? If so, the best way to get the information you need is to use the Table Browser to get the selected fields for your SNPs of interest and send that output to galaxy where you can use their intersection tool to intersect the SNPs with a genes track.
Click 'Tables' in the top blue menu bar and select your clade, genome, and assembly of interest. Then make the following selections: group: 'Variation and Repeats' track: latest SNP track for your assembly table: use the default table (snp###) region: genome identifiers: click 'upload list'; upload the file with your identifiers and click submit output format: selected fields from primary and related tables; and check the box next to Galaxy (to send output to Galaxy) Click 'get output'. Select the fields you want from table. You'll definitely want to select 'func' because this will provide you with the information you wanted about where the snp is located (coding, intron, etc) and probably probably also want the name, chrom, strand, chromStart, and chromEnd fields. Click 'done with selections' and then 'Send query to Galaxy'. From Galaxy, you can go to 'Get Data' and then 'UCSC Table Browser' and do a query to get all the genes from your gene track of choice. The query results will appear to the right of the page (where you should also see the data from your snp query that you sent over. Then click on the 'Operate on Genomic intervals' link on the left side and click on the 'Join' (the intervals of two queries side-by-side) link. Select the two queries that you just did to create a join between them. If the gene track data isn't showing up as an option for the join, click the 'Edit attributes' pencil icon of that query (in the history area on the right) and change the data type to 'interval'. The eye icon next to the results will allow you to display the data and you will be able to see the snps, their regions, their function Please don't hesitate to contact the mail list again if you have any further questions about the UCSC Genome Browser. For questions about using Galaxy please contact the Galaxy helpdesk via the following email: galaxy-user at bx.psu.edu Katrina Learned UCSC Genome Bioinformatics Group Prithvi Raj wrote, On 12/9/2010 7:23 PM: > Hi, > > Having got a satisfactory answer to my previous query, I have another quick > question for you. > > I have chromosome numbers and positions for the SNPs, but i need the gene > name and excat location (i mean, 3', 5', intonic or coding) of these SNPs > (approximate no. 200, 000). > > Can i have this information from UCSC genome browser, if yes, then how. > Please suggest. > > Thanks in advance ! > Sincerely, > Prithvi > > > ________________________________ > > UT Southwestern Medical Center > The future of medicine, today. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
