What is "dark cycles"?

[illuminaGA]

Dear All

I am new to NGS. I have a basic question. What is the dark cycles? How to set up the dark cycles running?

Thank you so much.

[mastal]

They are cycles during which only the chemistry is done, there is no measurement of fluorescence.

Below is a quote from the Illumina website:

http://support.illumina.com/sequencing/sequencing_instruments/hiseq_2000/questions.ilmn

As part of the answer to the question:
What is the workflow for dual indexing?


"Index Read 2 (i5): For paired-end flow cells, the Index 1 (i7) Read product is removed and the template anneals to the grafted P5 primer on the surface of the flow cell. The run proceeds through an additional seven chemistry-only cycles (no images are taken) followed by eight cycles of sequencing to read Index 2 (i5).
For single-read flow cells, the Index 1 (i7) Read product is removed and the Index 2 (i5) sequencing primer (HP9) is annealed to the same template strand. The run proceeds through eight cycles of sequencing to read the Index 2 (i5)."

[illuminaGA]

Thank you so much!

They are cycles during which only the chemistry is done, there is no measurement of fluorescence.

Below is a quote from the Illumina website:

http://support.illumina.com/sequencing/sequencing_instruments/hiseq_2000/questions.ilmn

As part of the answer to the question:
What is the workflow for dual indexing?


"Index Read 2 (i5): For paired-end flow cells, the Index 1 (i7) Read product is removed and the template anneals to the grafted P5 primer on the surface of the flow cell. The run proceeds through an additional seven chemistry-only cycles (no images are taken) followed by eight cycles of sequencing to read Index 2 (i5).
For single-read flow cells, the Index 1 (i7) Read product is removed and the Index 2 (i5) sequencing primer (HP9) is annealed to the same template strand. The run proceeds through eight cycles of sequencing to read the Index 2 (i5)."

[BHR]

Sorry to bump the old thread.

My question is, what is the purpose doing the dark cycle? The original template already binds to grafted P5 primer, why can't just go straight to the index 2 read?

[nucacidhunter]

Dark cycles are used to quickly fill the 7 base gap from graft 5’ end to first base of index.

[BHR]

Dark cycles are used to quickly fill the 7 base gap from graft 5’ end to first base of index.

Got it, thanks. leaving no loose ends...