Is this a overclustering?

[illuminaGA]

Dear All

I am currently at 18 cycle of 101+7+101 PE running.

I loaded 12pM sample and Phix(Lane4).

The intensity is ok in the first base. But from cycle 2,the intensity was dropping dramatically.

I also found the Base T thumbnail imagaes look strange.

I attached some pictures here.

What should I do now?

Thank you so much?

[GenoMax]

Is this MiSeq or HiSeq? What is the cluster density number?

You are not going to be able to do much if it is over-clustered. You will have to re-run.

[illuminaGA]

Here is other infomation.

Only the bottom looks normal.

[illuminaGA]

This is GAiix. cluster density is around 600.

Thank you so much.

Is this MiSeq or HiSeq? What is the cluster density number?

You are not going to be able to do much if it is over-clustered. You will have to re-run.

[illuminaGA]

Is this MiSeq or HiSeq? What is the cluster density number?

You are not going to be able to do much if it is over-clustered. You will have to re-run.

In the previous run. Some time we got cluster density around 1000+/- 50. And got high quality data.

But this time ,I don't konw why.

[GenoMax]

Guess you should let the run finish and see what the data looks like. One hits a bad flowcell once in a while so this could just be a one time issue.

[illuminaGA]

Guess you should let the run finish and see what the data looks like. One hits a bad flowcell once in a while so this could just be a one time issue.

Hi GenoMax, Thank you so much.

I have to stop the running since the run will not perform well.Illumina Techsupport recommended checking the fluidics on the system by performing a maintenance wash and measuring the delivered volume by lane.
I did it and fluidics were all good.

[andibody]

The last picture reminds me of problems we had with the mode scrambler.

[illuminaGA]

Thank you so much.

Illumina FSE will replace a new part for our GAiix.

The last picture reminds me of problems we had with the mode scrambler.

[cdalgard]

Did you ever figure out why you had a good first base report and then a significant decrease in intensities for Cycle 2?