We consistently get individual cycles with error rates 5-20% above the 'baseline' error rate followed by cycles with normal low error rates in the per tile error plots. Below is a representative, "normal" error plot on our GAI machine. Are we alone with this problem?
These error 'spikes' occur in all 8 runs we've done (phiX controls, human genomic samples, small RNAs), in all lanes and in a majority of the tiles. They are more common in later cycles and become more common from lane 1 towards lane 8 and seem to be more common towards the short ends of the flowcell. Tiles imaged in succession do not consistently show spikes in the same cycles. The type of error causing the spikes is that As are read as Cs. Since spikes are randomly distributed, the intensity plot for each lane looks normal (both level and decline).
I have contacted Illumina repeatedly about this issue but they cannot seem to do anything about it. Needless to say I would be very happy if anyone could come up with an idea about the cause of this problem it can be fixed.
These error 'spikes' occur in all 8 runs we've done (phiX controls, human genomic samples, small RNAs), in all lanes and in a majority of the tiles. They are more common in later cycles and become more common from lane 1 towards lane 8 and seem to be more common towards the short ends of the flowcell. Tiles imaged in succession do not consistently show spikes in the same cycles. The type of error causing the spikes is that As are read as Cs. Since spikes are randomly distributed, the intensity plot for each lane looks normal (both level and decline).
I have contacted Illumina repeatedly about this issue but they cannot seem to do anything about it. Needless to say I would be very happy if anyone could come up with an idea about the cause of this problem it can be fixed.
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