We have been facing this problem specifically with the Lane 8 of the GA2X Flow cell. Everytime we have the run, there is a recurrent problem with the Lane # 8. The intensity values are very inconsistent and there is a huge variation in the maxima and minima of the Intensities per tile, thus resulting in bigger Box plots per cycle. Has anyone in the GA2X community, face this problem? If yes, can this be explained? We could not get any explanation either from Illumina or from their local engineers.
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We sometimes get a loss of intensity in the right hand side tile of the lane 8at the right hand edge. We notice this more when loading the oil we follow the flow soon after beginning to load. If we dispense the oil in the same position at the bottom a little longer before moving the tip to follow the front edge of the oil, it's usually ok.
I heard that when the peltier comes down for the first cycle, and presses against the FC, the oil can recede slightly when the peltier moves up again. This causes a refraction change at the far right hand edge causing the loss of intensity. -
The larger intensity boxplots are just due to the higher intensity on the right hand edge of the flow cell so lane 8 has one half with a normal intensity and the half next to the edge has a higher intensity, every GAII I have seen has this. This should not effect your Q30 scores it is just the nature of the beast.
You can sometimes reduce this by running a tip along the edge of the right side to pull the oil over but it will not completely go away.Comment
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How much Oil do u usually load for a GA2X machine? Illumina usually recommends 150. But how much do u load?Comment
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We use the 150 ul. Generally it does not all get added to fill the gap between the flow cell and the prism.Comment
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Lane 8 issues
I too have had issues with quality scores and actual pass filter reads being zero on lane 8. Illumina has been great in helping me troubleshoot this issue. How I load the oil definitely came up. I typically only load 125ul. We are running a test flow cell now, all lanes phix, so I will post the results.Comment
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