bcl2fastq on windows?

[jdb]

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

[GenoMax]

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.

[WhatsOEver]

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.

[GenoMax]

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.

[WhatsOEver]

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.

[LarsB]

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