u Purge consumables for this run—Change the setting to purge consumables automatically after
the current run.
u Use run monitoring for this run—Change the setting to use run monitoring in BaseSpace.
7 Select Next.
Review Pre-Run Check
The software performs an automated pre-run check of the system. During the check, the following
indicators appear on the screen:
u Gray checkmark —The check has not been performed yet.
u Progress icon—The check is in progress.
u Green checkmark—The check passed.
u Red X —The check did not pass. For any items that do not pass, an action is required before you
can proceed. See
Resolve Automatic Check Errors
on page 44.
To stop an automated check in progress, select the Cancel button. To restart the check, select the
Retry button. The check resumes at the first incomplete or failed check.
To view the results of each individual check within a category, select the category tab.
Start the Run
When the automated pre-run check is complete, select Start. The sequencing run begins.
To configure the system to start the run automatically after a successful check, see
Set Run Setup
Options
on page 13.
Monitor Run Progress
1 Monitor run progress, intensities, and quality scores as metrics appear on the screen.
Figure 19 Sequencing Run Progress and Metrics
A Run progress— Shows the current step and number of cycles completed for each read. The
progress bar is not proportional to the run rate of each step. The estimated date and time of run
completion is shown at the bottom.
B Q-Score— Shows the distribution of quality scores (Q-scores). See
Quality Scoring
on page 56.
C Intensity— Shows the value of cluster intensities of the 90
th
percentile for each tile. Plot colors
indicate each base: red is A, green is C, blue is G, and black is T.
D Cluster Density (K/mm²)—Shows the number of clusters detected for the run.
Document # 1000000041922 v01
For Research Use Only. Not for use in diagnostic procedures.
24
NextSeq 550Dx Research Mode Instrument Reference Guide
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