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Old 04-05-2016, 02:53 PM   #8
Location: USA

Join Date: Aug 2013
Posts: 52

Originally Posted by sajoshi View Post
I think the libraries were prepared using Nextera. I did not make them, it was another user running on our machine. The run failed three time at the 300 cycle. I think he spiked 5%. He has had successful runs on MiSeq but using other kits and not this one. Illumina is troubleshooting the issue for me.
Do you mean it failed at the 300th cycle; eg at the end of one side of a 2x300 run?

You have to be more aggressive with the tech support if they aren't helpful. Ask for a PhiX run using a 2x300 kit. If that fails then it is definitively the machine's fault.

If you are using libraries with PhiX spike-in then it could be any number of factors.
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