Hello Sonja, You can use the Table Browser to retrieve the genome positions of the centromeres for the hg19. Go to the Table Browser (the blue "Tables" link at the top of the page) and make the following selections: clade: mammal genome: human assembly: Feb 2009 group: mapping and sequencing tracks track: gap table: gap region: genome output format: all fields from selected table (alternatively, you could choose "selected fields from primary and related tables" if you want to limit the fields in the output. Continue to follow the next steps. At the end, when you click "get output," you will be able to select the fields you wish to see before your results are displayed. For example, you might only want to see the data in chrom, chromStart & chromEnd and so you would only check those fields)
Next to "filter:" click the "create" and enter "centromere" in the "type does match" box. Then click submit. Back on the main Table Browser page, click the "get output" button. Your results should be a list of all of the centromeres (including their start and end locations) that are annotated in the hg19 assembly. You will notice that all the centromeres are 3 million base pairs each. The centromeres are very difficult to sequence (because they are heterochromatic) and so sequencing centers simply report them as gaps. Please let us know if you have further questions. Katrina Learned UCSC Genome Bioinformatics Group Sonja Althammer wrote: > Hello! > I need to obtain the centromeric positions of all chromosomes in hg19? > For h18 I could see the whole chromosome in a small image on the Genome > Browser. So I could click on both parts of the centromere and get the > positions manually. > Even better would be a table that gives the start and end position of each > human chromosome directly! > What I could find is a table for centromeric gaps which does not help me as > I want to locate the whole centromere. > I am looking forward to your answer! > Regards > Sonja Althammer > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
