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Question: Does Galaxy Have A Tool For Converting .Sra Files To Fastq Files?
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gravatar for Elwood Linney
5.8 years ago by
Elwood Linney • 180
Elwood Linney • 180 wrote:
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
galaxy • 6.4k views
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modified 2.3 years ago by tania • 0 • written 5.8 years ago by Elwood Linney • 180
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gravatar for Björn Grüning
5.8 years ago by
Björn Grüning • 350
Björn Grüning • 350 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=SR RXXXXXX&format=fastq Hope that helps, Bjoern -- 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/
ADD COMMENT • link written 5.8 years ago by Björn Grüning • 350
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
ADD REPLY • link written 5.8 years ago by Anton Nekrutenko ♦ 1.7k
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gravatar for tania
2.3 years ago by
tania • 0
tania • 0 wrote:

Hi guys, i was attempting to do as suggested above and i keep getting the errors:

Unable to fetch ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP051/SRP051844/SRR1747143&format=fastq <urlopen error="" ftp="" error:="" [errno="" ftp="" error]="" 550="" srr1747143&amp;format="fastq:" no="" such="" file="" or="" directory="">

I tried Using NCBI SRA tools and direct pasting and nothing works! What seems to be the issue?
ADD COMMENT • link written 2.3 years ago by tania • 0
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