does Galaxy have a tool for converting .sra files to fastq files?
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
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:
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-- 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: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
Hi: Alternatively you can note the SRA sequence identified and use Galaxy's EBI-SRA datasource to import data directly. a. Anton Nekrutenko http://www.galaxyproject.org 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:
-- 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: bjoern.gruening@pharmazie.uni-freiburg.de 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:
participants (3)
-
Anton Nekrutenko -
Björn Grüning -
Elwood Linney