Re: [galaxy-dev] Tools to download SRA datasets from GEO
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 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? >> >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tools to download SRA datasets from GEO
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? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tools to download SRA datasets from GEO
Do any tools exist to download GEO datasets from NCBI? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
