Hi Hao, As you suggest in your next email, the best way to obtain a list of genes and their gene position from a gene prediction track is to download the corresponding tables from our downloads server: http://hgdownload.cse.ucsc.edu/. Every assembly has a database directory that contains .txt.gz files, which are a dumps of every table in our database, and .sql files, which should help you determine each column headings for the corresponding table.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 8/6/10 8:48 AM, [email protected] wrote: > Dear Colleague, > > > Could you please advise how I can get a three column file. The first column > is the geneSymbol. The second and third column denote the chromosome and gene > position. The file I want to generate for all the hg18 genes looks like the > following: > > Symbol Chr hg18position > ABL1 9 132,579,089-132,752,883 > ABL2 1 177,335,085-177,378,834 > ACSL3 2 223,433,976-223,516,363 > AF15Q14 15 38673739-38705530 ... > > I can do some programming. I need to know which file(s) I need to program on > in order to get my desired files. > > > Thanks, > Hao Zheng > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
