Removing flowcell between two reads

[Sivakumar Gowrisankar]

Hi

Though it is not advisable, can we remove a flowcell and place it back between two reads of a run (say for paired-end run)?

Thanks
Siva

[Lee Timms]

You can remove the flowcell between reads 1 and 2 however you should not treat the run as paired end - you should analyze both reads as single read runs.

Lee

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[Yunchen Gong]

I agree, and that's because you introduce an offset too big for the pipeline to correct.

Yunchen

[Kevin M. Carr]

No, you absolutely cannot remove the flowcell mid run. The cluster template is determined only once, at the start of read 1. Unless you have some sort of super-power there is no way you could reposition the flowcell within the tolerances required.

Kevin M. Carr

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[Sivakumar Gowrisankar]

Thanks everyone! This is useful information.

[Lee Timms]

You should start a new run after first base incorporation from R2.  

Once first base has completed, stop your run and open a new recipe.  Recalibrate, find edge etc in the new recipe.

[J]

On a GA, no. It's much more likely to work on a HiSeq, though as you
say, it's not a great general practice.