Hi Steve, Thank you very much for your detailed and quick reply. I really appreciate it. I tried the second way you gave me in the below and it worked.
thanks! Laura ________________________________ From: Steve Heitner <[email protected]> To: Laura Smith <[email protected]>; [email protected] Sent: Tuesday, June 19, 2012 1:39 PM Subject: RE: [Genome] Canonical transcripts for REFSEQ Hello, Laura. I just wanted to point out that the solution I sent you earlier does not produce a canonical set directly from RefSeq. We do not have such a set. The method I suggested is simply a means of obtaining RefSeq IDs from our own canonical set. If this method is satisfactory to you, a slight modification to the previous steps may provide you with more RefSeq IDs than the original method. Instead of the previous step 5, perform the following: 5. In the "Linked Tables" section, check the hg19.knownToRefSeq checkbox 6. Scroll down and click the "allow selection from checked tables" button 7. In the "hg19.knownToRefSeq fields" section, check the "value" checkbox 8. Click the "get output" button In addition, you may find the previously-answered mailing list question at https://lists.soe.ucsc.edu/pipermail/genome/2010-April/021815.html helpful. This answer assumes a degree of familiarity with command line tools. If you are not as comfortable with command line tools, you can also find an assortment of useful tools at Galaxy (http://galaxy.psu.edu/). Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: Steve Heitner [mailto:[email protected]] Sent: Tuesday, June 19, 2012 10:16 AM To: 'Laura Smith'; [email protected] Subject: RE: [Genome] Canonical transcripts for REFSEQ Hello, Laura. 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. We have a knownCanonical table associated with the UCSC Genes track. If you want the transcripts in terms of RefSeq IDs, you will have to link to an additional table. Please follow the below instructions: 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: UCSC Genes Table: knownCanonical Region: Select either "genome" for the entire genome or specify a region next to "position" Output format: selected fields from primary and related tables 3. Click the "get output" button 4. In the "Select Fields from hg19.knownCanonical" section, check the checkboxes for the fields you wish to display 5. In the "hg19.kgXref fields" section, check the hg19.refseq checkbox to display the associated RefSeq ID in your output 6. 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: [email protected] [mailto:[email protected]] On Behalf Of Laura Smith Sent: Tuesday, June 19, 2012 9:45 AM To: [email protected] Subject: [Genome] Canonical transcripts for REFSEQ Hello, I would like to get the canonical transcripts for REFSEQ. Is there a way to get this online from UCSC genome browser or a link to this data perhaps? If so, would it be possible for you to send me the directions to download it please? I looked at UCSC genome browser website, but couldn't figure out where the canonical transcripts are: REFSEQ. I would very much appreciate your help on this matter. Thank you, Laura _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
