Configure Genotyper for all users of your lab with the different options of the Settings module.
General
In General Settings, theme settings, graph settings, plate settings, history grid settings, summary settings, analysis settings and failed plate settings can be configured. All these settings are laboratory settings, and will be applied for all users.
Theme settings
Transitioning from legacy tools can be challenging for team members that have been used to specifics for multiple years. In Genotyper, 3 themes are available that allow you to make the switch easier.
Graph settings
From the Graph axes behaviour drop-down menu, you can choose how the graphs will be visualized:
Use uniform axes will result in a graph with the same length for the X- and Y-axis.
Fit around data and history will create a plot that fits both the data and the history.
From the Graph axes margin drop-down menu, you can choose how the graph margins behave.
Use automatic margins will leave a small margin around the outer datapoints, which may result in a negative value label on the axes.
Disable margins will leave no margin around the outer datapoints.
From the Graph grid lines drop-down menu, you can set whether to show grid lines by default or not.
Plate settings
From the Plate selection behavior drop-down menu, you can choose the default behavior of selection in the plate table in an opened analysis. Choose from:
First plate selected
All plates selected
No plates selected
From the Plate tracking behavior drop-down menu, you can choose whether plates should be tracked over assays.
History grid settings
From the History grid visualization behavior drop-down menu, you can choose to have the history grids shown by default or not.
From the History grid merge behavior drop-down menu, you can choose how history should be visualized in case more than one history grid is available for the selected plates. This can be the case if plates are read by a different instrument. This setting only influences the visualization of the history grid and does not impact the algorithm scoring.
Genotyper will always search for a unique history grid for the instrument and assay combination.
If no unique history grid is found and Merge applicable history grids is enabled, history grids of instruments used in this analysis are merged into one grid and shown.
If no unique history is found and Keep history empty is enabled, no history grid is shown.
Summary settings
From the Rich view drop-down menu, more information can be added for each assay and plate in the analysis matrix view. If this Rich View is enabled, a bar representing all available scores and their share in the total amount of samples is visualized.
Samples visualized in the bar are: the 3 Genotype scores (red, green, blue), uncalled samples, inconclusive samples, shortfall, bad samples.
Long PCR plate names and assay names may be too long to visualize. Choose the truncate direction: left or right.
Analysis settings
From the Read saving behavior, a user can adjust when a user chosen read should be saved:
Manual save only: when selecting a different read than the AI chosen one (for one or multiple plates), this will never be saved automatically.
Manual save and auto-save upon edits: when selecting a different read than the AI chosen one (for one or multiple plates), this will be be saved automatically after scoring samples on the selected plate(s).
Failed plate settings
Genotyper will ask for a reason when submitting a PCR plate as failed.
The reasons for failure that are available in the drop-down can be updated in this setting.
Manual review
In this menu thresholds for parameters can be set which will result in warning icons reminding you to review this plate manually.
A user can enable or disable a warning for Uncalled samples, Shortfall samples and Failed Control samples.
For every parameter, a threshold can be set above which a warning with chosen severity will be shown. These settings are general for all analyses that are imported.
To visualize the manual review settings at import time of an analysis, navigate to the assay matrix view, click on the Actions button and analysis settings.
UI Status mapping
In the sample status tab, a user can rename the sample statuses to be visualized in opened analyses, for all users of the same Genotyper environment.
Select the sample status you want to rename and the new name. Don’t forget to Save. These new names are used in the Genotyper application.
Tip:
To use the mappings in your export files, enable the setting Use UI status mapping in exports in Integrations > Global customizations.
Integrations
Imports
Choose which Import buttons should be available In your Analysis module.
Exports
Multiple export types related to specific instruments are available. Choose the type of export you want Genotyper to create upon exporting or authorizing an analysis.
For some types, specific settings are available that only apply for this export type.
Choose from:
Universal export
Grid export
Export detailed calls: By default, all datapoints that didn't receive an algorithm score or is no NTC, is classified as '?'.
Exclude master plate columns: columns MasterPlateName and MasterPlateWell will not be exported.
Fluidigm export
Intellics export
Global customizations
In the Settings module of Genotyper the following can be set to your preferences:
Format settings
Setting Enable colon addition for alleles separates alleles by a colon ‘:’ in the export file. Disable the setting to remove the ‘:’. (Applicable for all export types)
Setting Export as Y:X instead of X:Y will swap the allele labels for the heterozygous class. (Applicable for all export types)
By enabling Assay sorting from input file the assay sequence in the export file is the same as in the input file. We advice to use this when combined assays are analyzed together. (Applicable for grid and universal export)
Additional data settings
If your Genotyper input file contains metadata, the setting enable metadata in supported exports will make sure these columns are included in the export file as well.Applicable for grid and universal export.
To Export imported empty wells, make sure the empty wells are available as sample type 'Empty' in the input file. (Applicable for grid and universal export)
Status mapping
Use UI Status mapping in exports
Enable this setting to use the mappings set in Settings > UI Status mapping in your export file. (Applicable for all export types)
Column name mapping
Export custom column headers
Rename the column headers to make a better fit with your lab. (Applicable for grid and universal export)
Assay export mapping
The default XX, XY, YY export mapping for each genotype can be overridden here. (Applicable for all export types). Also for all available levels of ploidy, a default export mapping can be set here.
Tip: on the assay-level, export mappings can be overruled for that specific assay.
Export file name pattern
Define a custom export filename by adding custom text and variables. The filename field can be composed by dragging and dropping variables into the filename pattern or simply by clicking on each variable.
Positive controls
Genotyper supports different options to discover positive controls and to configure their expected call for each assay. This paragraph gives an introduction on the available options.
Please contact your Breed Bio representative to set the optimal configuration for your needs.
1. Controls configured in input file
For specific file formats (.gtd) we support sample types in the input file. This way Genotyper can recognize a sample as being a control.
The expected call for these controls can be
Specified in the input file. The sample will be visualized as a control sample (triangle) in the colour of the expected call.
As all information is available in the input file, no reference lines are trained to Genotyper.
Not specified in the input file. The sample will be visualized as a control sample (triangle) in the colour of the call given by the algorithm.
Upon authorizing, the result is trained to Genotyper and the positive control is automatically configured as a reference line with an expected call for each assay.
Next time this reference line is present in an analysis, the expected call is known and Genotyper can pass/fail the sample.
2. Controls configured in Genotyper
2.1 Detecting a positive control
Control discovery
Rules can be configured by which regular samples are recognized and handled as a positive control sample type, based on their sample name.
A common factor in the naming convention of controls is recommended, for example "PC_".
At this moment the control has no expected call yet and will be visualzed as a passed control with expected call 'uncalled'. The colour of the control sample will be as per the classification.
By authorizing the analysis, the result is trained to Genotyper and the positive control is automatically configured as a reference line with an expected call for each assay.
Next time this reference line is present in an analysis, the expected call is known and Genotyper can pass/fail the sample.
Reference lines
For each unique sample name a reference line can be configured. These can be configured via control discovery rules, or configured directly on the settings page.
2.1 Reference lines: expected calls
Unlike NTCs, by definition, Positive Controls require an "expected call" to verify the control. For reference lines configured in Genotyper, the expected calls are set up per assay; this can be achieved in 3 ways.
Learn automatically after authorizing
Manually editing in the assay details page
By importing the assay csv
Option 1: Learn "Expected calls" automatically
For Reference lines that have no expected call, the call will be learned automatically when authorizing an analysis, based on the scoring in that analysis.
In Assays, the Expected call is now automatically set.
(note that "Edited in" contains a link to the analysis that was used to set this value)
Option 2: Set reference lines' expected calls per assay manually
Go to the Assays module and open the assay of your interest.
In the tab Reference Lines, you will see the reference lines you’ve just configured
Per reference line, set up the expected call.
(note that "Edited in" says "Settings", because this expected call is set manually)
Option 3: Import a CSV with the expected calls per reference line and assay
Navigate to the Assays module and with the Actions dropdown, export assays
For each of your reference lines, a column is available with the header ‘ReferenceLine_{{YourReferenceLineName}}’
Filter for the selected assays and fill in the expected call
Following formats are accepted (only heterozygous example shown):
AlleleX:AlleleY, AlleleXAlleleY, AlleleY:AlleleX or AlleleYAlleleX
If the alleles names are empty, configure the expected call as X:Y or XY
With the Actions dropdown menu in the Assays module, Import the updated Assay spreadsheet as a CSV
For each analysis that is now imported in Genotyper, samples with a name defined as a Reference Line will be visualized as a triangle in the color of the defined expected call.
Tip:
The auto-create expected calls or auto-learn expected calls behavior can be disabled at authorization-time by checking "Disable reference line creation for this analysis".
Negative controls
By default, NTCs will be scored, validated, and added to history. This behavior can be overruled by defining fixed master plate position(s) for NTCs. As a result, NTCs on other master plate positions will not be scored, validated, nor added to history.
With the implementation of fixed NTCs, negative process controls that can assume 'any' result (i.e. process controls such as floating empty wells for visual verification of sample plates) can now be filtered out.
In this example, NTCs that re not master plate position H12, will not be scored, validated, nor added to history.