Question: Database Associated With Galaxy Server
gravatar for Jennifer Hillman Jackson
5.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Mitali, There is a rice genome available for use with most tools already on the public Main Galaxy server at ( On the tool form, for the option to select a reference genome, or on the Upload or Edit Attributes form when selecting genome/build, type in the keyword "rice" to bring up: Rice (Oryza sativa): oryza_sativa_japanica_nipponbare_IRGSP4.0 For genomes not included as built-in native indexes (perhaps you wish to use a different strain), a Custom reference genome can be also used with most tools on Main. Instructions are here: There are a few tools on Main that do not allow for Custom reference genomes - these have a fixed set of specified target genomes. Megablast is one such tool. To use an alternate genome with this tool and the few others like it, a local or cloud Galaxy is required. Instructions are here: If you need to add a reference genome to a local Galaxy (a cloud Galaxy would already include everything currently on Main), you can create the indexes yourself, or rsync our files for use in your instance. The rsync server also lists all genomes currently indexed on Main. Instructions are here: Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training
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