Hello, Alexander. You can find the information you're looking for 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 do what you're suggesting is a two-step process. First, you will want to determine the coordinates of the pseudoautosomal regions. The table you want to use currently exists only on our genome-preview server. 1. From http://genome-preview.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: Mapping and Sequencing Tracks Track: PAR Table: par Region: genome Output format: all fields from selected table 3. Click the "get output" button Next, you will want to list the SNPs that fall into the pseudoautosomal regions. 4. From http://genome.ucsc.edu, select "Tables" from the blue navigation bar at the top of the screen. 5. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Variation and Repeats Track: Select the SNP track of your choice Region: Click the "define regions" button and specify the regions listed in the output from step 3 Output format: Select "all fields from selected table" to list all fields or "selected fields from primary and related tables" to list only certain fields 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 Navarini, Alexander Sent: Tuesday, June 05, 2012 9:38 AM To: [email protected] Subject: [Genome] FW: liftOver help Importance: High Dear Kayla, how can I annotate the first field in the .BED file of the SNPs in the XY pseudoautosomal regions, with the position on X and on Y separately? Thanks, Alexander ---------------------------------------------------------------------------- ----------------------------- Alexander Navarini Dr.med. Dr.sc.nat., Dermatologist & Venereologist FMH UEMS EBDV Division of Genetics and Molecular Medicine, King's College London St John's Institute of Dermatology, Guy's Hospital, Great Maze Pond SE1 9RT London, United Kingdom [email protected]<mailto:[email protected]> From: Navarini, Alexander Sent: 03 June 2012 16:25 To: '[email protected]' Subject: liftOver help Importance: High Dear Kayla, I get an error message with the liftOver tool that I cannot understand. ./liftOver all_03_qc.gen hg18ToHg19.over.chain.gz all_03_qc_hg19.gen unMapped Reading liftover chains Mapping coordinates invalid unsigned integer: "rs9755941" I can transform my .BED files on your website just fine, so I'm puzzled. Could you please give me advice there? Thanks, Alexander I downloaded the liftOver executable just now and gave it permissions. wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chai n.gz ---------------------------------------------------------------------------- ----------------------------- Alexander Navarini Dr.med. Dr.sc.nat., Dermatologist & Venereologist FMH UEMS EBDV Division of Genetics and Molecular Medicine, King's College London St John's Institute of Dermatology, Guy's Hospital, Great Maze Pond SE1 9RT London, United Kingdom [email protected]<mailto:[email protected]> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
