Question: Does Galaxy Have A Tool For Converting .Sra Files To Fastq Files?
gravatar for Elwood Linney
5.8 years ago by
Elwood Linney180
Elwood Linney180 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
ADD COMMENTlink modified 2.3 years ago by tania0 • written 5.8 years ago by Elwood Linney180
gravatar for Björn Grüning
5.8 years ago by
Björn Grüning350 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. 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: Web:
ADD COMMENTlink written 5.8 years ago by Björn Grüning350
Hi: Alternatively you can note the SRA sequence identified and use Galaxy's EBI-SRA datasource to import data directly. a. Anton Nekrutenko
ADD REPLYlink written 5.8 years ago by Anton Nekrutenko1.7k
gravatar for tania
2.3 years ago by
tania0 wrote:

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

Unable to fetch <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 COMMENTlink written 2.3 years ago by tania0
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