Hiseq imaging problems - dark edge

[MLog]

Hi everyone,

I noticed a strange effect on our HiSeq - the lower intensity of A and C on left side of the swath (attached are two thumbnails illustrationg this).
This effect is not flowcell- or library-dependent - I ran several flowcells, PE and SR, with different libraries, and it is always the same thing.
The fact that this concerns only A and C nucleotides makes me think that something is wrong with the laser. However our FSE who checked the lasers recently says that they are OK.
Has anyone faced with similar problem?

[pmiguel]

Hi everyone,

I noticed a strange effect on our HiSeq - the lower intensity of A and C on left side of the swath (attached are two thumbnails illustrationg this).
This effect is not flowcell- or library-dependent - I ran several flowcells, PE and SR, with different libraries, and it is always the same thing.
The fact that this concerns only A and C nucleotides makes me think that something is wrong with the laser. However our FSE who checked the lasers recently says that they are OK.
Has anyone faced with similar problem?

Yes, we had this. Seems like the instrument was performing above spec, so we didn't really push Illumina to address it. After our 2500 upgrade it got a little worse, but still we were getting excellent results.

About 1 month back we had some mysterious issues getting a run started. I think it must have been run chemistry related, but we never nailed down a cause. Anyway, our Engineer came out late one day to see if he saw any issues with the instrument. He tuned the peltiers and aligned the optics. But said neither was even close to be sufficient to explain our issues. However our next runs looked great -- all problems seemed to have resolved. Also the dark edge phenomenon was substantially reduced.

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Phillip