at the first incomplete or failed check. To view the results
of each individual check within a category, select the “v”
icon to expand the category (see Note 24).
40. When the automated check is complete, select Start. The
sequencing run begins.
41. Monitor run progress, intensities, and quality scores as metrics
appear on the screen (see Note 25).
(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. Use the time
remaining in the upper-right corner to determine actual
duration.
(b) Q-score—Shows the distribution of quality scores
(Q-scores). See Quality Scoring on page 45 of the Illumina NextSeq 500 System Guide (Document
#15046563v06).
(c) Intensity—Shows the value of cluster intensities of the
90th percentile for each tile. Plot colors indicate each
base: red is A, green is C, blue is G, and black is
T. Colors match base indicators used in the Sequencing
Analysis Software (SAV).
(d) Cluster Density (K/mm
2 )—Shows the number of clusters
detected for the run.
(e) Clusters Passing Filter (%)—Shows the percentage of clusters passing filter. See Clusters Passing Filter on page 45 of
the Illumina NextSeq 500 System Guide (Document
#15046563v06).
(f) Estimated Yield (Gb)—Shows the number of bases projected for the run.
Cycles for Run Metrics
Run metrics appear at different points in a run.
l
During the cluster generation steps, no metrics appear.
l
The first five cycles are reserved for template
generation.
l
Run metrics appear after cycle 25, including cluster
density, clusters passing filter, yield, and quality scores.
Depending on the analysis configuration selected,
an icon appears on the screen during the run to indicate the data transfer status (see Notes 26 and 27).
Sequencing Analysis Viewer
The Sequencing Analysis Viewer software shows
sequencing metrics generated during the run. Metrics
appear in the form of plots, graphs, and tables based on
data generated by RTA and written to InterOp files.
RNAseq Workflow
503
of each individual check within a category, select the “v”
icon to expand the category (see Note 24).
40. When the automated check is complete, select Start. The
sequencing run begins.
41. Monitor run progress, intensities, and quality scores as metrics
appear on the screen (see Note 25).
(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. Use the time
remaining in the upper-right corner to determine actual
duration.
(b) Q-score—Shows the distribution of quality scores
(Q-scores). See Quality Scoring on page 45 of the Illumina NextSeq 500 System Guide (Document
#15046563v06).
(c) Intensity—Shows the value of cluster intensities of the
90th percentile for each tile. Plot colors indicate each
base: red is A, green is C, blue is G, and black is
T. Colors match base indicators used in the Sequencing
Analysis Software (SAV).
(d) Cluster Density (K/mm
2 )—Shows the number of clusters
detected for the run.
(e) Clusters Passing Filter (%)—Shows the percentage of clusters passing filter. See Clusters Passing Filter on page 45 of
the Illumina NextSeq 500 System Guide (Document
#15046563v06).
(f) Estimated Yield (Gb)—Shows the number of bases projected for the run.
Cycles for Run Metrics
Run metrics appear at different points in a run.
l
During the cluster generation steps, no metrics appear.
l
The first five cycles are reserved for template
generation.
l
Run metrics appear after cycle 25, including cluster
density, clusters passing filter, yield, and quality scores.
Depending on the analysis configuration selected,
an icon appears on the screen during the run to indicate the data transfer status (see Notes 26 and 27).
Sequencing Analysis Viewer
The Sequencing Analysis Viewer software shows
sequencing metrics generated during the run. Metrics
appear in the form of plots, graphs, and tables based on
data generated by RTA and written to InterOp files.
RNAseq Workflow
503