Hi all,
I'm new to the SEQanswers community; from what I have seen from browsing this is an awesome resource for all those dealing with NGS. So, thank you in advance for any advice you can throw my way.
I run an Illumina Genome Analyzer IIx, with a Paired End module. It seems everytime I start a run, another issue crops up. I started a run early this month but was unsatisfied with Q30 scores, so I stopped it. Turns out the machine needed a new green laser motor. Once installed, I ran a PhiX flow cell using a 2x33 recipe. Our Q30 metric for the entire run was above 95% which is awesome...
So, from here I rehyb'd the original flow cell and loaded it onto the GA with full confidence. I applied the oil, checked for leaks, wiped down the peltier, the whole nine yards. The first base report was alarming however, with standard deviations above 50,000 for cluster densities. I contacted the FAS who did a share-my-desktop; he pumped the reagents manually and reran the calibration, find edge, and read prep 1. The bottom row of tiles that are imaged showed something very strange. One tile would be extremely blurry, then the tile directly adjacent to it would be clear as day. The blurry images only occurred on the bottom row, but once again, it was not every tile or even both tiles in a lane. Has anyone out there experienced this before? Of course I am in contact with the company, but any advice or hypothesis is appreciated.
Many thanks
JB
I'm new to the SEQanswers community; from what I have seen from browsing this is an awesome resource for all those dealing with NGS. So, thank you in advance for any advice you can throw my way.
I run an Illumina Genome Analyzer IIx, with a Paired End module. It seems everytime I start a run, another issue crops up. I started a run early this month but was unsatisfied with Q30 scores, so I stopped it. Turns out the machine needed a new green laser motor. Once installed, I ran a PhiX flow cell using a 2x33 recipe. Our Q30 metric for the entire run was above 95% which is awesome...
So, from here I rehyb'd the original flow cell and loaded it onto the GA with full confidence. I applied the oil, checked for leaks, wiped down the peltier, the whole nine yards. The first base report was alarming however, with standard deviations above 50,000 for cluster densities. I contacted the FAS who did a share-my-desktop; he pumped the reagents manually and reran the calibration, find edge, and read prep 1. The bottom row of tiles that are imaged showed something very strange. One tile would be extremely blurry, then the tile directly adjacent to it would be clear as day. The blurry images only occurred on the bottom row, but once again, it was not every tile or even both tiles in a lane. Has anyone out there experienced this before? Of course I am in contact with the company, but any advice or hypothesis is appreciated.
Many thanks
JB
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