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Old 07-28-2011, 05:19 AM   #1
ocs
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Default RNAseq sample files

Hello folks,

does anyone know where I can find some sample files for RNAseq (human genome)? I'm planning to do some analysis on them to test out a pipeline.
I couldn't find anything but maybe I'm searching the wrong terms ...

Any help is appreciated!

Thanks is advance,
Oliver
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Old 07-28-2011, 05:30 AM   #2
fkrueger
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Hi Oliver,

just go to the NCBI Gene Expression Omnibus page (http://www.ncbi.nlm.nih.gov/geo/) and enter "RNA-Seq Homo sapiens" or something similar into the query field "DataSets". Hope this helps.
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Old 07-28-2011, 05:55 AM   #3
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That helped a lot, thanks!
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Old 07-29-2011, 08:54 AM   #4
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I have some issues finding fastq files of these experiments. I searched GEO and SRA but I can only find processed data. I found a tutorial to extract fastq files from SRA but it seems to be out of date: http://code.google.com/p/altanalyze/wiki/DownloadFASTQ

Where can I find fastq-files from RNA-seq experiments?

Any help appreciated,
thanks in advance,
Oliver
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Old 07-29-2011, 12:31 PM   #5
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Hi Oliver,

SRA data can easily be converted into FastQ files using the SRA toolkit (http://trace.ncbi.nlm.nih.gov/Traces...are&s=software). The toolkit provides a program called fastq-dump, and it really is as easy as this:

/path/to/sra-toolkit/fastq-dump archive.sra

Hope it works.
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Old 07-29-2011, 04:40 PM   #6
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Thanks, that works great!
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