does Galaxy have a tool for converting .sra files to fastq files?

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does Galaxy have a tool for converting .sra files to fastq files?

Elwood Linney
Hello,  I would like to download some GEO files that complement my own research with zebrafish embryos but apparently GEO is now only providing .sra flles.

For a not very experienced unix person, does Galaxy have a tool for this or is there a clear description somewhere else of how to do it for someone who is not a bioinformaticist?

Thanks,

el linney
Duke University Medical Center

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Re: does Galaxy have a tool for converting .sra files to fastq files?

Björn Grüning
Hi,

you can try to import your SRA directly as fastq files. Paste that URL
in the upload tool and modify the XXXX number.

http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRRXXXXXX&format=fastq

Hope that helps,
Bjoern

> Hello,  I would like to download some GEO files that complement my own
> research with zebrafish embryos but apparently GEO is now only
> providing .sra flles.
>
> For a not very experienced unix person, does Galaxy have a tool for
> this or is there a clear description somewhere else of how to do it
> for someone who is not a bioinformaticist?
>
> Thanks,
>
> el linney
> Duke University Medical Center
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/

--
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: [hidden email]
Web: http://www.pharmaceutical-bioinformatics.org/

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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Re: does Galaxy have a tool for converting .sra files to fastq files?

Anton Nekrutenko
Hi:

Alternatively you can note the SRA sequence identified and use Galaxy's EBI-SRA datasource to import data directly.

a.


On Jan 31, 2013, at 8:58 AM, Björn Grüning wrote:

Hi,

you can try to import your SRA directly as fastq files. Paste that URL
in the upload tool and modify the XXXX number.

http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRRXXXXXX&format=fastq

Hope that helps,
Bjoern

Hello,  I would like to download some GEO files that complement my own
research with zebrafish embryos but apparently GEO is now only
providing .sra flles.

For a not very experienced unix person, does Galaxy have a tool for
this or is there a clear description somewhere else of how to do it
for someone who is not a bioinformaticist?

Thanks,

el linney
Duke University Medical Center
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

--
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: [hidden email]
Web: http://www.pharmaceutical-bioinformatics.org/

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/