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  • bcl2fastq on windows?

    Hi all,

    I am new to Illumina data. I have several BCL files and I need to convert them to FASTQ. I found the bcl2fastq program but it says it is only supported on Linux operating systems, and I have windows based computers. Has anyone tried to get it to work under windows? Any suggestions or tricks would be appreciated.

    Thanks,

    J

  • #2
    Do you have the entire raw data folder? What kind of Illumina data is this?

    If at all feasible I suggest that you go back to whoever gave you these files and ask them to do the conversion for you.

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    • #3
      The best way would be to switch to linux and ban windows

      You may also simulate linux (virtualbox) or use cygwin which gives some linux functionalities under a win env.

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      • #4
        If this is a one time deal I am not sure if it is worth going through all the trouble a VM/bcl2fastq install is going to cause.

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        • #5
          Originally posted by GenoMax View Post
          If this is a one time deal I am not sure if it is worth going through all the trouble a VM/bcl2fastq install is going to cause.
          Of course not, but its the only reliable way to get it working while staying in windows.

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          • #6
            Hi, I just found this page with a bcl2fastq tool for windows

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