Hello, The data from the track Affy Zebrafish has a primary identifier of qName. In the Table browser , checking out "View table schema", I can see that no tables will link from this track to the gene name as displayed in the RefSeq track. Instead, an overlap comparison must be done.
There are three methods to choose from: http://genome.ucsc.edu/FAQ/ 1) In Table browser, create a custom track containing the Affy Zebrafish consensus sequences of interest. starting with RefSeq Genes, perform an intersection query using the custom track, and output all records from Affy Zebrafish with the overlap specified, in the output linking in the refFlat.geneName field. The downside to this query is that which Affy Zebrafish consensus captured which refFlat.geneName is not recorded. 2) In Table browser, perform an interval intersection using Galaxy. Create a custom tracks containing track coordinates (one containing the geneName and one containing the Affy consensus sequence), select output format BED, and send to Galaxy. There, convert the file format to interval and join based on genomic overlap. Identifiers from both datasets will be preserved. Instructions/FAQ help for Galaxy is available here: http://g2.trac.bx.psu.edu/ 3) Using a combination of Table browser and unix tools: download the appropriate tables, examining the contents in the Table browser to learn the file names and structure. join the data based on genomic overlap using your own script or one of ours. FAQ to the source tree utility set: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities Thank you, Jennifer Jackson UCSC Genome Bioinformatics Group Zhengpeng Wu wrote: > Hi, > > I am dealing with zebrafish microarray dataset. > After gene selection, I get a list of 'GeneID'. > My 'Zebrafish Array gene info' file is built upon DanRer4 version of > Zebrafish genome of UCSC. > My question is: > "how to find the location and sequence information of these genes in UCSC > database?" > Because I cannot find any table in: > http://hgdownload.cse.ucsc.edu/goldenPath/danRer4/database/ > having 'gene id' field. > > Could you please help me with this question? Thanks a lot! > > Sincerely, > Zhengpeng Wu > Tsinghua University, Beijing, China > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
