gbrowse_import_ucsc_db (1)

This creates a framework data source for one of the genomes known to the UCSC Genome Browser. You can then modify the data source configuration file, add your own data, and so forth. Provide the name of a UCSC genome build and optionally a description to display in GBrowse.

To get started, find the desired data source by going to http://genome.ucsc.edu/cgi-bin/hgGateway and using the "clade" and "genome" menus to navigate to the desired species and build number. You will find the data source name in the blue box below the navigation controls. Look for something like this:

D. melanogaster Genome Browser – dm3 assembly (sequences)

The data source name appears before the word "assembly", in this case "dm3".

[options] <UCSC genome build> [<Description>]

To get a list of all sources recognized by UCSC appears type:

browse_import_ucsc_db --list

Options:

  --remove-chr Remove the 'chr' prefix from all chromosome names
  --list       List data sources

Example: $0 hg19 'Human genome (hg19)'

Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging Lincoln Stein - GBrowse