Hello,
For several months now, we observed on our GAIIx that the intensities for the second read in a paired end run (V4 kits) are often below the intensities of the last cycle of the first read. Before we always obtained a first cycle intensity for read 2 between 100 to 70% of the the first cycle intensity for read 1 (as it is normally expected).
We have had some extreme runs where the 1st cycle intensity of read 1 is 386 and for the second read it drop at 53 for the phiX lane. The engineer from Illumina checked already several times the peltier and re calibrated its temperature and alignment. Until now the problem isn't solved.
The quality of the results for read 2 for the phiX lane still fall within the specifications of Illumina on % error Rate but are typically twice as high as the error rate for read 1.
I checked all the runs we did before this phenomenon started and we always observed almost exactly the same error rate for read 1 and 2.
As the results are within specifications Illumina pretends their is no problem, but we have the very strong feeling that the machine is running below optimal.
Does anyone else has observed similar problems and if yes how were they solved?
For several months now, we observed on our GAIIx that the intensities for the second read in a paired end run (V4 kits) are often below the intensities of the last cycle of the first read. Before we always obtained a first cycle intensity for read 2 between 100 to 70% of the the first cycle intensity for read 1 (as it is normally expected).
We have had some extreme runs where the 1st cycle intensity of read 1 is 386 and for the second read it drop at 53 for the phiX lane. The engineer from Illumina checked already several times the peltier and re calibrated its temperature and alignment. Until now the problem isn't solved.
The quality of the results for read 2 for the phiX lane still fall within the specifications of Illumina on % error Rate but are typically twice as high as the error rate for read 1.
I checked all the runs we did before this phenomenon started and we always observed almost exactly the same error rate for read 1 and 2.
As the results are within specifications Illumina pretends their is no problem, but we have the very strong feeling that the machine is running below optimal.
Does anyone else has observed similar problems and if yes how were they solved?
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