How to use lentil genotypic matrix tool to find genotypic data for your reference germplasm
Overview
Teaching: 5 min
Exercises: 5 minQuestions
How to find genotypic data for the given germplasm?
Objectives
Providing a step by step demonstration on how to search from genotypic matrix tool
Go to the Lentil Genotype Matrix Tool
When you land on the Knowpulse home page https://knowpulse.usask.ca click on “Genotypes” at the top of the page, this will scroll you down to the genotypes section. Then you can click on “Lentil Genotypes” to access the Lentil Genotype Matrix Tool on the same page.
Find genotypic data for your reference germplasm
Enter the name of each germplasm you are interested in by typing it in the textfield labelled germplasm, ILL 8006 and CDC Milestone in this example. Make sure the correct species is selected to the right of the textbox. To add more then one germplasm, click the green + button.
After entering ILL 8006 in the top germplasm textfield, you will notice that it autocompleted as you type. Then click the green + button and enter CDC Milestone in the second textfield which appears.
Each time you click the green + button or search, the genotypic data for the listed germplasm will be shown.
Key Points
Log in KnowPulse with your user account before searching.
How to compare two germplasm and how to find varients from the interested region
Overview
Teaching: 10 min
Exercises: 10 minQuestions
How to search for sequence varients between two selected germplasm?
How to view genome within a given region?
Objectives
Providing a step by step demonstration on how to compare two germplasm and how to find sequence varients in an interested region.
Restrict the Sequence Variants to polymorphic between your germplasm
Underneath germplasm, there is a filter to restrict to polymorphic variants. This filter compares two germplasm and only shows variants with different genotypic calls.
For our example, we would select ILL 8006 in the first drop down and CDC Milestone in the second drop-down to see only sequence variants with differing genotypes (i.e polymorphic variants) between these two germplasm.
Click Search to see the results.
Restrict to your trait-implicated Region of the Genome
The second section of the filter criteria available for the genotype matrix allows you to enter the region of the genome you are interested in. Once you click search, the genotype matrix will only show sequence variants found in this region.
In our example, the region of interest is LcChr4:1875000-2075000. To enter this, we place LcChr4 for the Sequence Name, 1875000 for the start position and 2075000 for the end position.
Key Points
Log in KnowPulse with your user account before searching.
How to see subset of your interested set of varients
Overview
Teaching: 5 min
Exercises: 5 minQuestions
How to use additional filter criteria section to help find subset?
Objectives
Providing a step by step demonstration on how to use additional filter criteria section to help find subset of interested.
(Optionally): Restrict to specific variants.
Say you are interested in a specific set of variants and would like to see that subset. You can enter the specific variant names by expanding the Additional Filter criteria section then clicking Search.
Key Points
Log in KnowPulse with your user account before searching.
This step is optional.