bcl2fastq on windows?

jdb · 10-12-2015, 03:47 PM

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 · 10-12-2015, 04:38 PM

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 · 10-13-2015, 03:44 AM

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 · 10-13-2015, 04:14 AM

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 · 10-13-2015, 04:25 AM

Quote:

Originally Posted by 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.

Of course not, but its the only reliable way to get it working while staying in windows.

LarsB · 11-22-2019, 06:00 AM

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

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10-12-2015, 03:47 PM	#1
jdb Junior Member Location: ca Join Date: Oct 2015 Posts: 1	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

10-12-2015, 04:38 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	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.

10-13-2015, 03:44 AM	#3
WhatsOEver Senior Member Location: Germany Join Date: Apr 2012 Posts: 215	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.

10-13-2015, 04:14 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	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.

11-22-2019, 06:00 AM	#6
LarsB Member Location: France Join Date: Feb 2013 Posts: 12	Hi, I just found this page with a bcl2fastq tool for windows