Hi Jason, You could use the table browser to do part of what you want to do. You could create a custom track containing your rsIDs and then you can intersect it with a gene prediction track to obtain the genes with coding regions that intersect with the SNPs in your custom track. However, there are a few shortcomings with this method: 1. You will only get genes that have SNPs in the coding region of a gene (not those that are near SNPs). 2. The results won't show which rsID corresponds to which gene.
To get all the information you are interested in, you need to go through our collaborator, Galaxy, and use their more advanced data manipulation tools. A link to Galaxy is here: http://main.g2.bx.psu.edu/ First create a custom tracks for your gene prediction track of interest and for your list of rsIDs. Then you can use Galaxy's tool to "Join the intervals of two queries side-by-side". The "join intervals" function is under the "Operate on genomic intervals" section on the left-hand side. Create Gene Prediction Custom track to send to Galaxy: Open the table browser and choose the clade, genome, and assembly of your choice (e.g. Mammal; Human; Mar. 2006). Then make these additional selections: group: Gene and Gene Prediction Tracks track: Choose your track of interest (e.g. UCSC Genes, RefSeq Genes, etc.) table: the automatically populating table is a good place to start (this is the primary table; for more information about the table, click "describe table schema") region: genome output format: all fields from selected table Select "Send output to Galaxy" Create SNP track with your rsIDs to send to Galaxy: Choose your clade, genome, and assembly of interest and make these additional selections: group: Variation and Repeats track: SNPs(130) table: snp130 region: genome Next to "identifiers" click the "paste list" button to paste a list of rsIDs or click "upload list" to upload a file containing all the rsIDs. Click submit. output format: all fields from selected table Select "Send output to Galaxy" I hope this helps you. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Jason Ting wrote: > Dear UCSC Genome Browser, > > Is there a way to query the Table Browser for closest genes/exons, based on a > list of rsIDs? > > Best Regards, > > Jason Ting > > > > _________________________________________________________________ > Hotmail: Powerful Free email with security by Microsoft. > http://clk.atdmt.com/GBL/go/171222986/direct/01/ > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
