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Question: NCBI genome to Galaxy
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gravatar for RACHAMPION
2.4 years ago by
RACHAMPION • 10
RACHAMPION • 10 wrote:

I am trying to download

Brachypodium distachyon strain Bd21 chromosome 2, Brachypodium_distachyon_v2.0, whole genome shotgun sequence

from NCBI http://www.ncbi.nlm.nih.gov/nuccore/NC_016132.2.

NCBI gives me a result in compressed format (.gz)

Do I need to uncompress this to get it in to Galaxy?

How can I get this into a local library so that it will be available for multiple analyses?

Is there a Galaxy site that works best?

Thanks
rna-seq data transfer from ncbi • 806 views
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modified 2.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.4 years ago by RACHAMPION • 10
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gravatar for Jennifer Hillman Jackson
2.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If using the free public server Galaxy Main (http://usegalaxy.org), the dataset can be uploaded in gz format. It will uncompress automatically and can be used directly from the history as a custom genome to map. To assign as a "database", promote the custom genome to a custom build. The fasta genome itself can be copied between histories (without using additional account quota disk) and shared publically. The "build" (database) is available to just you, but others can create their own. How to: https://wiki.galaxyproject.org/Support#Custom_reference_genome

Many other public Galaxy sites will allow the same actions. List: https://wiki.galaxyproject.org/PublicGalaxyServers

If working on a local/cloud Galaxy where you are admin, the same actions are available or the data could be loaded into a Shared Data Library and used from there. Options: https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

Hopefully this helps! Jen, Galaxy team
ADD COMMENT • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k
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