Hi Chris, I'm sorry, didn't think about the "define regions" function in the Table Browser would not having extra logic to account for insertions. If you instead create a custom track of your regions and intersect it with the SNP table, you should be able to get the results you want.
To do this, click the "Add custom tracks" button, and then either paste or upload your regions. The regions will need to be in BED format (note that the start position is decreased by one base in this format): http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED Your custom track data should look something like this (the 4th column is optional): chr1 9959747 9959748 rs1220382 chr1 9959848 9959848 rs58501900 etc. The first line in this example is a regular SNP at position 9959748. The second line is an insertion between position 9959848 and 9959849. Once you have the custom track loaded, select it in the Table Browser and hit the "intersection: create" button. Choose the SNP table from the drop-down menus and make any other decisions about how you want the intersection to work on that page. Your output should be the reasons you specified that indeed have a SNP annotated in the SNP track. If you had a name in the name field in your BED file, you will see that in the output. If you would rather have the name of the SNP from dbSNP, you can do the intersection the other way: first choose the SNP table in the Table Browser and create an intersection with your custom track. I hope this helps. Please let us know if you have any additional questions. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/10/10 15:32, Chris Dias wrote: > Thank-you for your reply. > I've tried this but was not successful. > I have the reference position and chromosome position of possible SNPs. When > I define the position, the program requests I add a position greater than 1 > nucleotide. If I have the reference position of nucleoide changes, how else > would I be able to check whether they are known SNPs? It's a long list and I > was hoping there is some automated way to do this on UCSC genome browser. > Thank-you, > Chris > > On Mon, Oct 25, 2010 at 4:37 PM, Brooke Rhead <[email protected]> wrote: > >> Hi Chris, >> >> You can do this with the Table Browser ( >> http://genome.ucsc.edu/cgi-bin/hgTables). Select the assembly you wish to >> use, and then the Variation and Repeats group, and the SNP track and table. >> For "region" hit the "define regions" button and enter your list of >> positions. Choose your output format, and then hit "get output". >> >> You should see all of the SNPs that lie within the regions you entered. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 10/23/10 22:47, Chris Dias wrote: >> >>> Hi, >>> >>> I'd like to know if with a list of reference positions I can any coincides >>> with a know SNP position. >>> >>> Thank-you >>> Chris Dias >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
