dark edges

[josdegraaf]

Hi,

During our training run on the hiSeq we see quite a lot of dark side/edges in the lanes of the flow cell. Anybody else seen this? I first heard a certain batch of flow cells is affected but ours was not from this lot. Anybody hat a HiSeq flow cell without this?

Thanks,

[AnotherHTS]

Hi josdegraaf,

The gradient effect with darkened edges is something that we have observed to varying degrees on all of our Hi-Seq runs.

I believe this has been mentioned previously in the following thread:

http://seqanswers.com/forums/showthread.php?t=6294

[csquared]

Illumina just released an email stating that there have been manufacturing problems with the HiSeq flowcells and they are working on it. The dark edges are one of the observations with lesser quality flowcells. The issue seems to cause the greatest effect at longer read lengths (greater than 50). The newer flowcells definitely are better and the gradation from side-to-side is less (but not totally eliminated). I think there are a couple more things at play here other than just flowcell quality.

We have had maybe one or two out of 10 or 12 flowcells NOT have the dark edge problem but all of the flowcells have been a little different. Some had more issues with the top or bottom surface or front or back, etc.

[josdegraaf]

Thanks guys, I recieved the email.