Hello, Bin. I would recommend using our Table Browser to do this. If you are unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
The strategy will be to create the list of 5' UTR regions as a custom track and then create an intersection between our GC Percent track and the custom track. To do so, perform the following steps: 1. Browse to http://genome.ucsc.edu/cgi-bin/hgTables 2. Set the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownGene Region: Select "genome" for the entire genome. Selecting the entire genome will create an extremely large file, however, so it might be better to break it up by chromosome. Also, you will see later that output is limited to 10,000,000 data points, so breaking up by chromosome is the optimal method. To specify chromosome 1 only, click "position" and enter "chr1" (without the quotes) in the text box. Output format: custom track 3. Click the "get output" button 4. At the top of the screen in the "name=" field, you can specify the name of your custom track. You can also just leave the default name. 5. In the "Create one BED record per" section, click "5' UTR Exons" 6. Click the "get custom track in table browser" button 7. Change the following options: Group: Mapping and Sequencing Tracks Track: GC Percent Table: gc5Base 8. On the "filter" line, click the "create" button 9. Change "Limit data output to" to 10,000,000 and click the "submit" button 10. On the "intersection" line, click the "create" button 11. Change "group" to "Custom Tracks" - the custom track you just created should automatically become selected in the "track" field 12. Click the "submit" button 13. Set "output format" to "data points" 14. You can specify a filename on the "output file" line to save your output to a file or you can leave this blank and view your output in the Table Browser 15. 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 Wang, Bin Sent: Tuesday, July 24, 2012 12:49 PM To: [email protected] Subject: [Genome] Questions regarding base composition calculation Dear Sir/Madam, I downloaded all human 5'UTR sequences from your database. Is there a tool to calculate the overall GC composition of human 5'UTRs? Is there a tool to calculate base compositions of each sequence automatically? Thank you for your help, Bin _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
