Hello, Minou. It is not possible to add a name column to your output using the Table Browser. Here are some previously-answered mailing list questions that describe how to do similar tasks using Galaxy, a tool that works in conjunction with the Table Browser. If you have questions about Galaxy, contact their helpdesk at [email protected].
https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026083.html https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025251.html https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013512.html You may also consider simply taking the RefSeq IDs from the output of your first Table Browser query and making a second query to match your list of RefSeq IDs with their gene names. 1. Next to "identifiers," click the "paste list" or "upload list" button to enter your RefSeq IDs 2. Set "output format" to "selected fields from primary and related tables" 3. Click the "get output" button 4. Check the "name" and "name2" fields 5. Click the "get output" button. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: Minou Bina [mailto:[email protected]] Sent: Wednesday, January 25, 2012 7:59 AM To: [email protected] Cc: Steve Heitner Subject: Re: [Genome] track CpG islands Thank you Steve Heitner The procedure worked! How can I include a column listing the name of the genes as well (i.e. ID4)? Minou Bina Purdue University ----- Original Message ----- From: "Steve Heitner" <[email protected]> To: "Minou Bina" <[email protected]>, [email protected] Sent: Monday, January 9, 2012 5:03:20 PM Subject: RE: [Genome] track CpG islands Hello, Minou. You can do this by using our Table Browser. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. To find the genes that correspond with CpG islands, you'll need to perform an intersection. This "intersects" the CpG island table with the table containing the genes you're interested in and only displays the results where the CpG islands overlap with those genes. One tricky thing with intersections is that it lists the output in the format of your main table only (in step 2 below) - not the intersect table (in step 4 below). This means that if you want results in terms of the CpG islands and their coordinates, you need to use the CpG island table as your main table. If you want results in terms of the genes and their coordinates, you need to use the gene table (such as refGene or knownGene) as your main table. For this example, let's assume you're interested in human gene IDs from the RefSeq Genes track. Perform the following steps: 1. From http://genome.ucsc.edu, select "Tables" from the blue navigation bar at the top of the screen. 2. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: RefSeq Genes Table: refGene Region: Select either "genome" for the entire genome or specify a region next to "position" 3. Next to "intersection," click the "create" button 4. Select the following options: Group: Regulation Track: CpG Islands Table: cpgIslandExt 5. Click the "submit" button 6. Next to "output format," select "BED - browser extensible data" 7. Click the "get output" button 8. Click the "get BED" button You can experiment to see which options work best with your needs. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Minou Bina Sent: Monday, January 09, 2012 10:23 AM To: [email protected] Subject: [Genome] track CpG islands Hi Would you please provide intruction for how to obtain the coordinates of CpG islands and the corresponding genes from database. Thank you Minou Bina Purdue University _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
