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Old 10-12-2015, 03:47 PM   #1
jdb
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Default 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
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Old 10-12-2015, 04:38 PM   #2
GenoMax
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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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Old 10-13-2015, 03:44 AM   #3
WhatsOEver
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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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Old 10-13-2015, 04:14 AM   #4
GenoMax
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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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Old 10-13-2015, 04:25 AM   #5
WhatsOEver
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Quote:
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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