Hello Laura,

The ENCODE data is available via FTP hosted by UCSC. This is the main portal:
http://genome.ucsc.edu/ENCODE/

Follow the downloads link, then scroll down to the RNA-seq tracks. Click on the tracks you are interested in to locate the directories containing both the UCSC tracks and the source fastq data.

Once local to your computer, load into Galaxy in batch as a Data Library, then import datasets from libraries into histories to work with them. Data Library instructions are in our wiki. Because of the size of the data, you will most likely want to use the "Upload directory of files" option explained in the second link, once your environment is configured.

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

Hopefully this helps!

Jen
Galaxy team

On 10/16/12 1:44 PM, laura lafontaine wrote:
Hi everyone,

I'm new in Galaxy and I want to know if is possible download whole
rna-seq data from ENCODE project to my local galaxy instance (I have a
disk of 5 To) . If yes, would you explain me how I can do this?

Thank you in advance for your answer,

L


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The Galaxy User list should be used for the discussion of
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