Hi Mahdi, You will first need to download the column of identifiers from the gene table (refGene). You can do this via the Table Browser or MySQL command line. To do this from the Table Browser, make the following selections:
clade: Mammal genome: Human assembly: hg19 table: refGene region: genome output format: selected fields from primary and related tables Click get output. On the following page, select "name" then click get output. This will give you a list of refSeq identifiers. Next, you will want to sort this output, you can use a Unix command to do this. Then, sort your list of identifiers. Finally, you can use the comm command in Unix to compare the two lists: comm list1 list2 Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 6/22/2012 9:27 AM, Mahdi Ghani wrote: > To whom it may concern; > > I get no output from the UCSC table browser when I paste a list of ~2000 > identifiers and receive a warning/error message instead indicating that > almost 100 of given identifiers have no match in the table browser. Neither > full list of the error causing identifiers nor any output for the matched > identifiers is provided by the table browser. Pushing the "OK" button in the > warning message also doesn't give the output for the matched identifiers. > > > > However for the smaller datasets, I could receive the output only when I > clean the input list from the errors that are indeed provided in the warning > messages one by one. This approach would be apparently difficult for the > large datasets. > > > > I appreciate your help to solve this problem. > > > > Thank you in advance, > > > > Mahdi Ghani, MD > > University of Toronto > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
