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  • 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

  • #2
    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.

    Comment


    • #3
      That helped a lot, thanks!

      Comment


      • #4
        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 I found a tutorial to extract fastq files from SRA but it seems to be out of date: http://code.google.com/p/altanalyze/wiki/DownloadFASTQ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

        Comment


        • #5
          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.

          Comment


          • #6
            Thanks, that works great!

            Comment

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