Tools to download SRA datasets from GEO

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Tools to download SRA datasets from GEO

ryang
Do any tools exist to download GEO datasets from NCBI?



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Re: Tools to download SRA datasets from GEO

Hans-Rudolf Hotz
Hi

Are you looking for any special GEO data, which is not mirrored at the
ENA? If not, you can probaly use the  "Get Data" -> "EBI SRA" tool,
which is part of the installation.

Also, have you looked at the toolshed? e.g.
https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit


Regards, Hans-Rudolf



On 02/04/2015 04:44 PM, Ryan G wrote:

> Do any tools exist to download GEO datasets from NCBI?
>
>
>
>
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Re: Tools to download SRA datasets from GEO

ryang
Thanks Hans-Rudolf.  I didn't see the EBI SRA link before.  But not sure what will do what I want.  I want to be able to plug in an SRA # and have the tool download the data and prep it for analysis.  Right now, it looks like I need to click through the EBI website to get the data.  I found a tool in the toolshed but haven't had a chance to look at it. That is my next step.

On Thu, Feb 5, 2015 at 3:18 AM, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi

Are you looking for any special GEO data, which is not mirrored at the ENA? If not, you can probaly use the  "Get Data" -> "EBI SRA" tool, which is part of the installation.

Also, have you looked at the toolshed? e.g.
https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit


Regards, Hans-Rudolf



On 02/04/2015 04:44 PM, Ryan G wrote:
Do any tools exist to download GEO datasets from NCBI?




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