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The run biosamples tab contains a list of all the biosamples in the run. Use this option when:
You want a quick way to view all the biosamples in a run.
You want to see more detail about your biosamples, such as library, project, yield, or FASTQ files.
You can then select a biosample, library, pool, project, or FastQ Dataset from the table to view more details.
BaseSpace Sequence Hub groups your data by project, biosample, analysis, and run.
To view a list of runs in your account, select Runs.
To view a list of projects in your account, select Projects.
To view a list of analyses in your account, select Analyses.
To view a list of biosamples in your account, select Biosamples.
To view a list of Demo Data available for import into your account, select Demo Data.
The run samples tab contains a list of all the samples in the run. Use this option when:
You want a quick way to view all the samples in a run.
You want to see more detail about your samples, such as the analysis or project.
You want to view details and files for an individual sample. Click the sample name to access the sample details page.
Available only for indexed runs, the Indexing QC page provides indexing QC results for the run. View unexpected results for a sample, or confirm that all indexed samples are properly represented.
The first section contains a table that summarizes the indexing performance for the selected lane.
Total Reads: Total number of reads.
PF Reads: Total number of clusters passing filter.
% Reads Identified (PF): Percentage of clusters passing filter that are assigned to an index.
% Reads Undetermined: Percentage of clusters passing filter that could not be assigned to an index.
CV: Coefficient of variation for the number of counts across all indexes.
Min: Lowest representation for any index.
Max: Highest representation for any index.
The graph displays the % Reads Identified (PF) Per Index for the selected lane.
The second section shows % Reads Identified (PF) Per Index in the Per Index table.
Index: A unique number BaseSpace Sequence Hub assigns to each index for display purposes.
Sample ID: The sample ID assigned to an index in the sample sheet.
Library Name: The library assigned to an index in the sample sheet.
Index 1 (i7): The sequence for the first index read.
Index 2 (i5): The sequence for the second index read.
% Reads Identified (PF): Percentage of clusters passing filter that are assigned to the index.
This tab allows you to view the sample sheet that is tied to this run. Use this option when you want to view the associated sample sheet to make sure it was set up properly.
From the Run Overview Page, select the Sample Sheet tab.
If the sample sheet contains errors, use the Fix Sample Sheet procedure to make corrections and requeue the analysis.
In BaseSpace Sequence Hub, you can view and download individual base calls, images, and other run files. For information about downloading a package of run files, see Download Run Data Files.
Select the Files tab from a run page to view the run files directory.
Click a folder name to view nested folders/files.
Select a file name to preview the file.
[Optional] To download the file, select Download.
Projects are the containers for data sets, which can include FASTQ, BAM, and VCF files. They can be associated with other biosamples, runs, analyses, and other entities inBaseSpace Sequence Hub.
The Projects tab lists the projects in your account.
The Run Summary tab shows basic information about the run in the top section, including status of the run & QC checks, quality scores, yield, instrument type, run owner, and run creation date.
A link to the Latest Analysis is also provided in the top section, and a list of prior analyses are shown in the lower section.
The Run & Lane Metrics page has the overall statistics about the run. Use this option when you want to view information about the run, such as percent alignment, cycles, and densities.
The following metrics appear in the top table, Per Read Metrics:
The following metrics are available in the Per Lane Metrics table:
The Runs page lists your active or planned runs. These runs can include runs that you own and runs shared with you.
Permissions for runs and projects are separate. Sharing a project does not mean that you share the runs in that project.
To open the runs list, select the Runs tab. Runs that require attention appear above the runs list.
Selecting a run name opens a summary of the run. The following tasks to manage runs are also available from the Runs page:
Plan a Run — Plan an instrument run. For more information, see and .
Share and Transfer Run Data — Share runs with a collaborator. For more information, see .
Download Run — Download run files. For more information, see Download Run Data Files.
Requeue Sample Sheet — Fix sample sheet errors and requeue the analysis. For more information, see .
Requeue FASTQ Generation — Fix indexes and requeue the analysis. For more information, see .
Delete Run Data — Delete run files. For more information, see .
Metric
Description
Cycles
The number of cycles in the read.
Yield
The number of bases sequenced, which is updated as the run progresses.
Projected Yield
The projected number of bases expected to be sequenced at the end of the run.
Aligned
The percentage of the sample that aligned to the PhiX genome, which is determined for each level or read independently.
Error Rate
The calculated error rate of the reads that aligned to PhiX.
Intensity Cycle 1
The average of the A channel intensity measured at the first cycle averaged over filtered clusters. For the NextSeq 500 System, the red channel is used.
%Q ≥ 30
The percentage of bases with a quality score of 30 or higher, respectively. This chart is generated after the 25th cycle, and the values represent the current cycle.
Metric
Description
Clusters PF
The percentage of clusters passing filtering, +/- 1 standard deviation.
%Q ≥ 30
The percentage of bases with a quality score of 30 or higher, respectively. This chart is generated after the 25th cycle, and the values represent the current cycle.
Yield
The number of bases sequenced which passed filter.
Tiles
The number of tiles per lane.
Error Rate
The calculated error rate, as determined by the PhiX alignment. Select Subsequent columns display the error rate for cycles 1–35, 1–75, and 1–100.
Error Rate @cycle
The error rate for cycles 1–35, 1–75, and 1–100. Select the Error Rate value to view this metric.
Cycles Err Rated
The number of cycles that have been error-rated using PhiX, starting at cycle 1. Select the Error Rate value to view this metric.
Aligned
The percentage that aligned to the PhiX genome. Select the Error Rate value to view this metric.
Reads PF
The number of clusters (in millions) passing filtering.
Total Reads
The number of clusters (in millions). Select the Reads PF value to view this metric.
Density
The density of clusters (in thousands per mm2) detected by image analysis, +/- 1 standard deviation.
Phas./Prephas.
The value used by RTA for the percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read. For MiSeq and NextSeq, RTA generates phasing and prephasing estimates empirically for every cycle. The value displayed here is therefore not used in the actual phasing/prephasing calculations, but is an aggregate value determined from the first 25 cycles. For most applications, the value reported is very close to the value that is applied. For low diversity samples or samples with unbalanced base composition, the reported value can diverge from the values being applied because the value changes from cycle to cycle.
Phasing Slope/Offset, Prephasing Slope/Offset
The best-fit slope and offset of the phasing/prephasing corrections, calculated from the entire read.
Intensity
The average of the A channel intensity measured at the first cycle averaged over filtered clusters.
Status
The QC status for the run. Select the QC status to view detailed QC results.
The Analyses List contains a list of analyses in a project. Use this option when you want to navigate to details regarding a specific analysis result.
Navigate to an analyses list using one of the following methods:
To view all analyses, select Analyses.
To view analyses for a specific biosample, select the Analyses tab on the biosample details page.
To view analyses in a specific project, select Analyses from the project details page.
Select an analysis to see the results.
The Charts tab displays graphs of run metrics that update as the run progresses. Use these charts to monitor the quality of the run.
Data by Cycle graphs the progression by cycle of quality metrics during a run.
The Data by Cycle chart has the following features:
You can select the displayed metric, surface (if your system scans multiple surfaces), cycle, and channel (base) using the drop-down lists.
The chart is displayed with tailored scaling by default, or you can fix the Y-axis scale by selecting the Fix Scale checkbox.
Some metrics (% ≥Q20 and % ≥Q30) are monitored for a single cycle by default, or you can monitor the cumulative metrics (up to that cycle) by selecting the Accum checkbox.
You can focus on an area of interest by dragging to pan the view or using the mouse wheel to zoom in.
The following table details the possible metrics displayed in this chart. The available options vary by run.
Q-Score Distribution graphs the number of bases by quality score. The quality score is cumulative for the current cycle. Only bases from reads that pass the quality filter are included.
Use it to evaluate the Q-Score distribution for a run, which is an excellent indicator for run performance.
The Q-Score Distribution chart has the following features:
You can select the displayed read and cycle using the drop-down lists.
The chart is displayed with tailored scaling by default, or you can fix the Y-axis scale by selecting the Fix Scale checkbox.
Some metrics (% ≥Q20 and % ≥Q30) are monitored for a single cycle by default, or you can monitor the cumulative metrics (up to that cycle) by selecting the Accum checkbox.
You can focus on an area of interest by dragging to pan the view or using the mouse wheel to zoom in.
The Flow Cell Chart shows color-coded quality metrics per tile for the entire flow cell.
Use the Flow Cell Chart to judge local differences per cycle, per lane, or per read in sequencing metrics on a flow cell. It is also an easy way to see the %≥Q30 metric, which is an excellent single metric to evaluate a run. Do not use the Flow Cell Chart to look at downstream analysis metrics.
The Flow Cell chart has the following features:
You can select the displayed metric, surface (if your system scans multiple surfaces), cycle, and channel (base) using the drop-down lists.
The color bar to the right of the chart indicates the values that the colors represent.
The chart is displayed with tailored scaling by default, or you can fix the Y-axis scale by selecting the Fix Scale checkbox.
Some metrics (% ≥Q20 and % ≥Q30) are monitored for a single cycle by default, or you can monitor the cumulative metrics (up to that cycle) by selecting the Accum checkbox.
Tiles that have not been measured or are not monitored are gray.
You can focus on an area of interest by dragging to pan the view or using the mouse wheel to zoom in.
The following table details the possible metrics displayed in this chart. The available options vary by run.
Note the variable scales used on these different parameters.
The Data by Lane chart plots allow you to view quality metrics per lane.
Use the Data By Lane plot to examine the difference in quality metrics between lanes. Do not use the Data By Lane plot to look at alignment or variant calling analysis metrics.
The Data by Lane plot has the following features:
You can select the metric, surface, and read from the drop-down lists.
The plots show the distribution of mean values for a given parameter across all tiles in a given lane.
The red line indicates the median tile value for the parameter displayed. Blue boxes are for raw clusters, green boxes for clusters passing filter.
The box outlines the interquartile range (the middle 50% of the data) for the tiles analyzed for the data point.
The error bars delineate the minimum and maximum without outliers.
The outliers are the values that are more than 1.5 times the interquartile range below the 25th percentile, or more than 1.5 times the interquartile range above the 75th percentile. Outliers are indicated as dots.
You can focus on an area of interest by dragging to pan the view or using the mouse wheel to zoom in.
The following table details the possible metrics displayed in this plot. The available options vary by run.
The Q-Score Heatmap provides an overview of quality scores across cycles.
The Q-Score Heatmap has the following features:
The vertical color bar indicates the value that each color represents.
Scaling is specific to the run, representing 0%–100% of the maximum value.
The Biosamples page lists the biosamples in your account, the status of the biosample, and the projects that contain biosample data. Data generated from biosamples can be stored in more than one project, so a biosample can be listed multiple times in the biosamples list.
To open the Biosamples master list, click Biosamples in the top navigation bar.
Biosamples that contain aggregated data across runs and sample ID are locked to ensure their data are reviewed before being used in app analysis. For information about unlocking biosamples to enable analysis, see .
Setting
Description
Intensity
This chart shows the intensity by color and cycle of the 90% percentile of the data for each tile.
FWHM
The percentage of clusters for which the selected base (A, C, T, or G) has been called.
% Base
The percentage of clusters for which the selected base (A, C, T, or G) has been called.
% NoCall
The percentage of clusters that have no call.
% ≥Q20 and % ≥Q30
The percentage of bases with a quality score of > 20 or > 30, respectively. These charts are generated after the 25th cycle, and the values represent the current scored cycle.
Median Q-Score
The median Q-score for each tile over all bases for the current cycle. These charts are generated after cycle 25. Use this setting to examine the Q-scores of your run as it progresses. Because it relies on a single threshold, the %≥Q30 plot can be oversimplified.
Error Rate
The calculated error rate, as determined by a spiked in PhiX control sample. If no PhiX control sample is run in the lane, this chart is not available.
Phasing, Prephasing
The estimated percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read.
Legacy Phasing Rate, Legacy Prephasing Rate
The estimated percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read. Legacy rates consider only the first 25 cycles.
Corrected Intensity
The intensity corrected for cross talk between the color channels by the matrix estimation and phasing and prephasing.
Called Intensity
The intensity for the called base.
Signal to Noise
The signal to noise ratio is calculated as mean called intensity divided by standard deviation of noncalled intensities.
Option
Description
Intensity
This chart shows the intensity by color and cycle of the 90% percentile of the data for each tile.
FWHM
The average full width of clusters at half maximum (in pixels). Used to display focus quality.
% Base
The percentage of clusters for which the selected base (A, C, T, or G) has been called.
% NoCall
The percentage of clusters that have no call.
% ≥Q20 and% ≥Q30
The percentage of bases with a quality score of > 20 or > 30, respectively. These charts are generated after the 25th cycle, and the values represent the current scored cycle.
Median Q-Score
The median Q-score for each tile over all bases for the current cycle. These charts are generated after cycle 25. Use this setting to examine the Q-scores of your run as it progresses. Because it relies on a single threshold, the %≥Q30 plot can be oversimplified.
Density
The density of clusters for each tile (in thousands per mm2).
Density PF
The density of clusters passing filter for each tile (in thousands per mm2).
Clusters
The number of clusters for each tile (in millions).
Clusters PF
The number of clusters passing filter for each tile (in millions).
Error Rate
The calculated error rate, as determined by a spiked in PhiX control sample. If no PhiX control sample is run in the lane, this chart is not available.
Phasing, Prephasing
The estimated percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read.
Legacy Phasing Rate, Legacy Prephasing Rate
The estimated percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read. Legacy rates consider only the first 25 cycles.
% Aligned
The percentage of reads from clusters in each tile that aligned to the PhiX genome.
Occupied Count (K)
The total number of wells (in thousands) on the flow cell containing clusters with DNA usable for sequencing. Wells with at least nine G bases called in the first 10 cycles are considered empty. Low occupancy rate combined with low %PF may indicate the loading concentration is too low. High occupancy rate combined with suboptimal %PF may indicate the loading concentration is too high.
% Occupied
The percentage of wells (for patterned flow cells) or nonduplicated spots (for nonpatterned flow cells) on the flow cell containing clusters. Wells with at least nine G bases called in the first 10 cycles are considered empty.
Corrected Intensity
The intensity corrected for cross talk between the color channels by the matrix estimation and phasing and prephasing.
Called Intensity
The intensity for the called base.
Signal to Noise
The signal to noise ratio is calculated as mean called intensity divided by standard deviation of noncalled intensities.
Setting
Description
Density
The density of clusters for each tile (in thousands per mm2).
Clusters
The number of clusters for each tile (in millions).
Phasing, Prephasing
The estimated percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read.
Legacy Phasing Rate, Legacy Prephasing Rate
The estimated percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read. Legacy rates consider only the first 25 cycles.
% Aligned
The percentage of reads from clusters in each tile that aligned to the PhiX genome.
Occupied Count (K)
The total number of wells (in thousands) on the flow cell containing clusters with DNA usable for sequencing. Wells with at least nine G bases called in the first 10 cycles are considered empty. Low occupancy rate combined with low %PF may indicate the loading concentration is too low. High occupancy rate combined with suboptimal %PF may indicate the loading concentration is too high.
% Percent Occupied
The percentage of wells (for patterned flow cells) or nonduplicated spots (for nonpatterned flow cells) on the flow cell containing clusters. Wells with at least nine G bases called in the first 10 cycles are considered empty.
% PF
The percentage of clusters passing filter that are assigned to the index.
