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  • download with fastq-dump

    Hello everyone, I'm still new to RNAseq and I hope I can find someone to help me out with my question.

    I want to download RNAseq data (SRR) using SRA Toolkit which I already installed have on my macbook.

    this is the link from where I want to download the data



    I created a folder named processing and a subfolder named raw to where I want to put this data files.
    The command line is this one

    Patrizios-MBP:raw patrizio$ fastq-dump --outdir raw/ --split-3 --gzip SRR359063

    why do I get this?

    -bash: fastq-dump: command not found

    what is missing?

    thank you

  • #2
    The directory you have the program "fastq-dump" is likely not in your $PATH ( a set of directories that are automatically searched when you try to run something). You could try ./fastq-dump if the executable is in the directory where you are running this from.

    I suggest you save yourself the hassle and download fastq files directly from EBI-ENA here.

    You may want to learn unix basics by using this tutorial, if you are not familiar with command line.

    Comment


    • #3
      The suggestion turned out very useful and I'm downloading the files.
      I'm doing a course this days I wanted to practice and understand better by repeating what we did on my machine so it might be that the executable is not in my path?
      hope the informations below can tell that

      Patrizios-MBP:sratoolkit.2.9.4-mac64 patrizio$ ls
      CHANGES README-blastn README-vdb-config README.md bin example schema
      Patrizios-MBP:sratoolkit.2.9.4-mac64 patrizio$ ./fastq-dump
      -bash: ./fastq-dump: No such file or directory

      thank you

      Comment


      • #4
        Correct. That executable is likely in the "bin" directory that you see above. So you could have run it by saying
        Code:
        $ bin/fastq-dump --outdir raw/ --split-3 --gzip SRR359063

        Comment


        • #5
          It worked

          thank you!!

          Comment

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