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MiSeq System Guide
Important Notes Before Starting the Run
WARNING
The MiSeq is sensitive to vibration. Touching the instrument after starting a run could adversely affect
sequencing results.
After selecting Start Run, do not open the flow cell compartment or the reagent compartment doors, or
touch the instrument monitor except to pause the run. For more information, see
WARNING
Make sure to close all files on the MiSeq before starting a run, and do not open files during a run.
Monitor the Run
During a run, monitor run detail using the Sequencing screen on the instrument. The Sequencing screen is
view-only.
Other options to monitor a run include:
Sequencing Analysis Viewer (SAV) installed on a computer independent of the instrument computer. A
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network connection is required. For more information, see
Alternatively, if you are connected to BaseSpace, the run can be monitored using SAV in BaseSpace.
Local Run Manager for monitoring the run remotely if the instrument is connected to the same network.
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Local Run Manager shows run progress and sequencing information (Total Clusters, % Clusters PF, Read
1 and Read 2 %>= Q30, and Last Scored Cycle). For more information, see
on page
7.
1
On the instrument Sequencing screen, monitor run progress, intensities, and quality scores.
Run Progress—Shows run progress in a status bar and lists the number of cycles completed.
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Intensity—Shows the value of cluster intensities of the 90
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The graphic in the Intensity area represents the number of tiles and number of surfaces being imaged:
If the flow cell is imaged on the top surface only, a single-column graphic appears.
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If the flow cell is image on the top surface and bottom surface, a 2 column graphic appears.
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A Indicates 2 tiles, top surface only
B Indicates 4 tiles, top and bottom surface
Q-Score All Cycles—Shows the average percentage of bases greater than Q30, which is a quality
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score (Q-score) measurement. A Q-score is a prediction of the probability of a wrong base call. Q-
scores are calculated after cycle 25.
Q-Score
Probability of Wrong Base Call
Q40
1 in 10,000
Q30
1 in 1,000
Document # 15027617 v04 Material # 20024228
For Research Use Only. Not for use in diagnostic procedures.
Pause a Run on page
Sequencing Analysis Viewer on page
Local Run Manager Software
th
percentile for each tile.
43.
8.
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