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gbrowse_import_ucsc_db - Online in the Cloud

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This is the command gbrowse_import_ucsc_db that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


browse_import_ucsc_db - Creates a framework data source

DESCRIPTION


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".

USAGE


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

OPTIONS


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


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

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