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I am sequencing a whole genome on MinION. I have used this flow cell for 6 hours for the phage lambda control. That gave me around 300,000 reads. I started a 48h sequencing run on the same flow cell after washing it. The sequencing has been going on for 1 day and 21 hours. It is not producing any reads at the moment (Strand = 0). The number of single pores is also 0. Can I "Stop acquisition" without negatively affecting the results?

The image below is a screenshot taken from MinKNOW, the software used to control the MinION.

Pore description and read summary

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Yes, you can click "stop acquisition" and your run won't be negatively affected. All of the reads are saved as they are generated. I am not sure how this will impact live basecalling though if that is something that you do.

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    $\begingroup$ Live basecalling for the uncalled reads will continue until all have been called, or the application is quit. $\endgroup$ – gringer Mar 4 '18 at 8:06
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Yes, you can stop the run and it should not affect the base calling. We normally do the runs and then do the base calling after the run has completed.

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