Hello Agnes, To do a full (outer) join, this would be a good query path:
1) Load a BED file that contains the coordinates and the identifier as a Custom Track. A BED6 (six column) file is recommended so that genome strand is used. Format of BED file: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 Load as a Custom track with a simple track line: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks 2) Go to the Table browser and export both the RefSeq primary table (refGene) and your custom track to Galaxy. The RefSeq track is in the track group "Gene and Gene Predictions". Your data will be in the track group "Custom tracks. For each track separately, use the default options except change the output format to BED and check the box for Galaxy. Then "get output". It will load in Galaxy. 3) Once both datasets are in Galaxy, click on the pencil icon in the box containing each data set and rename the data format as "interval". Next, use the tool Operate on Genomic Intervals -> Join. The result can be shared (Options -> Share or Publish) or used for more analysis. Please feel free to contact the mailing list support team again if you would like more assistance. Warm regards, Jen UCSC Genome Browser Support On 7/28/10 11:35 AM, Agnes Williams wrote: > Hi, > I wonder if you could give me some tips about the most efficient way to get > the list of RefSeq (and/or UCSC) genes from thousands of range of > coordinates. The ideal output would be the one containing my identifier (of > the specific coordinate range), and the list of genes which overlap the > corresponding coordinates. I've been exploring the Table Browser, but > haven't found a way to do this in efficient manner. Would you have some > suggestions about the best way of doing this? > > many thanks in advance, > AW > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
