Marker Menu

When Markers are available for the KDDart implementation and configuration being used, KDManage will display the Marker menu as illustrated:

Marker menu

The topics in this section are as follows:

  1. Genotyping Marker Process - Describes Marker processing with KDDart
  2. DNA Management - Describes how to use the DNAManagement window
  3. Marker Data Management - Describes how to use the Marker Data Management window
  4. Marker Maps - Describes how to use Marker Map window

Genotyping Marker Process

The steps for preparing, ordering and storing genotypic analysis data in KDDart are described in the following table:

Step Activity Action
1 Define a group of samples for genotyping Select KDManage -> Marker -> Marker Data Management -> Add Marker Data Management
2 Download file (equivalent to the sample tracking file for the Online Ordering) Select the download button export_btn
3 Submit the sample tracking file for the order in the Online Ordering System. Optional genotyping service (ie DArT)
4 Prepare specification, submit file, sign, pack and ship DNA.
5 Genotyping service performs DNA analysis
6 Genotyping service notification that results are ready
7 Log into the Online Ordering and download the result file to a local/network location.
8 Use KDCompute to upload the result file to the KDCompute server for processing Select KDCompute -> File Manager -> Upload Files -> Select file and upload
9 Use KDCompute to import the data into KDDart Select KDCompute -> Submit a Job - > Import/Export Marker Data -> Import Marker Data -> Complete the form and submit the job
10 Check job status for successful import Select KDCompute -> File Manager -> submitted_jobs -> select job number -> download and view file(s)

Table notes:

  • DArT provides an optional genotyping/profiling service
  • Bold items within the Action column represent menu/selection text.

DNA Management

Select the DNA Management option (within the top Marker menu) to display the following window:

DNA Management window showing Add DNA plate button (select to zoom)

Add DNA Plate

To add a new DNA plate, select the Add DNA Plate button located on the DNA Management window as illustrated:

The Add DNA Plate window (select to zoom)

Field descriptions to assist with completing the form are displayed in the following table:

Field Mandatory Description
Trial Name M Trial that this plate is associated with. Upon selecting an exisiting trial, this will display the relevant plates to this trial.
Creation date M Date the genotyping service was created
Plate layout   CSV file containing plate name, row, column and genotype name columns.
Tissue M Tissue used in this plate

Plates as in the following illustration may be removed using the Remove Plate button at the bottom left.

Also individual cells may be edited or removed as required.

Field Mandatory Description
Plate 1 Name M Name for this iteration of plate
Plate 1 Description   Description of the plate
Plate 1 Storage Location   Location where the plate is stored
Plate 1 Tissue   Tissue used in this plates
Marker data management - plate (select to zoom)

Edit Well Plate

Selecting a Well will display the Edit Well Plate window, as displayed in the following illustration, where the well may be Edited or Removed using the buttons on the window.

Note: Hovering the mouse above a well will display the Trial Unit Position and the Specimen Name.

Marker data management - Edit well plate (select to zoom)

Marker Data Management

Select the Marker Data Management option (within the top Marker menu) to display the following window:

Marker Data Management table (select to zoom)

Add Marker Data Management

To add a new Marker Data management genotyping/profiling entry select the Add Marker Data Management button located on the Marker Data Management window as illustrated:

Add marker data management window (select to zoom)

Field descriptions to assist with completing the form are displayed in the following table:

Field Mandatory Description
Marker Data Management Name M Text string to describe the genotyping service
Description   Additional description of the the genotyping service
Manager Name   A designated manager for the genotyping service who is defined in KDDart Contacts
Selected plates M Plates from DNA Management selected for this Marker Data. Drag and drop plates from the “Plate List” table to add specific plates to this Marker Data.
Access Fields M Access Settings and Permissions

Plates as in the following illustration may be removed using the Remove Plate button at the bottom left.

Also individual cells may be edited or removed as required.

Field Mandatory Description
Plate 1 Name M Name for this iteration of plate
Plate 1 Description   Description of the plate
Plate 1 Storage Location   Location where the plate is stored
Marker data management - plate (select to zoom)

Edit Well Plate

Selecting a Well will display the Edit Well Plate window, as displayed in the following illustration, where the well may be Edited or Removed using the buttons on the window.

Note: Hovering the mouse above a well will display the Trial Unit Position and the Specimen Name.

Marker data management - Edit well plate (select to zoom)

Upload dataset file

To upload a new dataset to a Marker Data Management Group, select the Upload dataset button upload-btn in the Actions column for the required Group.

Upload dataset file window (select to zoom)

Note

For referencing the CSV file contents, column and row numbering commences with zero.

Tip

After selecting a file to upload, the file contents will be displayed underneath the form. This can be used to refer to the correct columns as required.

Field Description
CSV Data Set File Browse to locate and select the appropriate CSV file for import.
Plate Name Row The row where that the contains the plate names.
Well Row Position Row The row where that the contains the well row positions.
Well Column Position Row The row where that the contains the well column positions.
Header Row The row where that the contains the headers.
Marker Name Column The column where that the contains the marker names.
Sequence Column The column where that the contains the sequences.
Meta Data Start Column The first column in the CSV file containing meta data for import.
Meta Data End Column The last column in the CSV file containing meta data for import.
Data Start Column The first column in the CSV file containing data for import.
Data End Column The end column in the CSV file containing data for import.
Data Set Type The type of dataset, as defined in Type definitions.

List Marker Datasets of Group

To list all datasets in a Group, select the List datasets button list-btn in the Actions column for the required Group.

Upload dataset file window (select to zoom)

Visualise dataset with heatmap

To Visualise a dataset with a heatmap, select the Visualise dataset button heatmap-btn in the Actions column for the required Marker dataset of a Group.

Visualise dataset with heatmap window after filtering and sorting (select to zoom)

Data can be further filtered and sorted to retrieve more specific data. Visualised data can also be downloaded as an SVG file for further use.

Download dataset

To download, select the Visualise dataset button heatmap-btn in the Actions column for the required Marker dataset of a Group.

Download dataset window (select to zoom)
Field Description
Format Type The format of the dataset will be downloaded in. In standard installations, this will either be CSV or Flapjack. Extra formats can be added with extra development.
Marker Meta Data Field List Chosen marker meta data fields to include in download. Leave blank to include all.
List of DNA Extracts Chosen DNA Extracts to include in download. Leave blank to include all.
List of Marker Chosen markers to include in download. Leave blank to include all.

Data can be further filtered and sorted to retrieve more specific data.

Submit samples to genotyping vendor

If KDManage has bee configured with a vendor ID, users will be able to submit samples to the vendor from Analysis Group plates. To submit, select the Sample Submission to genotyping vendor button sample-btn in the Actions column for the required Analysis Group.

Field Description
BrAPI Genotyping Vendor Base URL The URL for Genotyping Vendors. These must be configured by System Administrator.
Source Field for Sample Id How samples will be identified
Authentication Token Authentication token from vendor.

Download genotyping result from vendor

If KDManage has bee configured with a vendor ID, users will be able to download genotyping results to the vendor for Analysis Group. To submit, select the Download genotyping from vendor button sample-down-btn in the Actions column for the required Analysis Group.

Marker Maps

Select the Marker Map option (within the top Marker menu) to display the following window:

Marker Map table (select to zoom)

Add Marker Maps

To add a new Marker Map, select Add Marker Map button located on the Marker Map window as illustrated:

Add new Marker Map window (select to zoom)

Field descriptions to assist with the completing the form are displayed in the following table:

Field Mandatory Description
Map Name M Text string to describe the Marker Map
Map type M The type of Marker Map, as defined in Type definitions.
Map Software   Name of software used to create map
Model Reference Informations   Model reference info - for physical maps
Map Description   General description of the map
Map Parameters M Map parameters (also software parameters) used for creation

Import Marker Map Position

To add a new Marker Map Position, select the Import Marker Map Position button KDMan-import-Btn.

Import new Marker Map Position window (select to zoom)

Note

For referencing the CSV file contents, column and row numbering commences with zero.

Tip

After selecting a file to upload, the file contents will be displayed underneath the form. This can be used to refer to the correct columns as required.

Field Description
Marker Map Position File Browse to locate and select the appropriate CSV file for import.
Marker Name Column The column where that contains the Marker Names. Note: markers must match the ones contained in the selected Analysis group.
Contig Name Column The column where that contains the Contig names
Contig Position Column The column where that contains the Contig positions
Analysis Group The Analysis group associated with uploaded Marker Map Positions. Note: Analysis group must have a least one dataset.