Crossing Simulation

Crossing Simulation estimates the variance and expected value of progenies to help you select the best parent crosses. This simulation has 4 steps:

1. Phase genotype file
2. Select parents to cross
3. Generate linkage map template
4. Select model

Phase genotype file

Crossing simulation requires a phased genotype file. Phasing involves assigning alleles (A, C, T, G) to the maternal and paternal chromosomes. This process reduces the number of false positive matches of SNPs.

What you need:

a. Genotype file

Steps:

1. In the Project Files page, click on a GENOTYPE file.

   

2. You will be redirected to the file's overview page. This page contains basic file information, as well as utility functions (Download Linkmap Template, Phasing, Resolve Synonym)

   

3. Click Phasing.

   

4. A new file will be created for the phased genotype file. Enter a new file name and click Save.

   

5. You will be redirected back to the file's overview page. By default, the phased vcf file is saved in the same folder as the original genotype file. In the example below, the original file is saved in the other folder. Click other to access the phased genotype file.

   

6. Genotype file is being phased, indicated by the PROCESSING status. Refresh the page to check the latest status.

   

7. Phasing is sucessful. This genotype file can be used for Crossing Simulation.

   

Select parents to cross

In order to run the simulation, a list of parent crosses (crossing table file) is required. Detailed file information can be found here.

What you need:

a. Crossing table file

Steps:

1. In the Project Files page, click Upload Crossing table file.

   

2. File was uploaded in Project Files.

   

Generate linkage map template

A linkage map file is also required for Crossing Simulation. Detailed file information can be found here.

What you need:

a. Genotype file (phased or unphased)

Steps:

1. In the Project Files page, click on a GENOTYPE file.

   

2. You will be redirected to the file's overview page. This page contains basic file information, as well as utility functions (Download Linkmap Template, Phasing, Resolve Synonym)

   

3. Click Download Linkmap Template.

   

4. A form will be displayed, requiring the following inputs:

   • Linkage map position
     • Fill up linkage map position by dividing by: This will calculate the linkage map position of each SNP (Dividing an SNP's physical position by a fixed recombination rate - bp/cM (base pair / centiMorgan))
     • Leave linkage map position blank: This will not calculate the linkage map position
   • File name: Automatically generated. Can be modified.

   

5. Select an option and click Save. The linkage map will be downloaded your local machine.

   

6. Linkage map file was downloaded.

   

7. Upload the linkage map to your Project Files.

   

8. Linkage map file was uploaded to your Project Files.

   

Create a cross simulation

What you need:

a. Evaluated Model
b. Genotype file - phased
c. Crossing table file
d. Linkage map file

Steps:

1. On the sidebar to your left, click Crossing Simulation

   

2. On the Crossing Simulation page, click Simulate

   

3. Crossing Simulatoin page will be displayeed, requiring you the following inputs:

   a. GS Model - an evaluated GS model
   b. Genotype file - a genotype file that has been phased
   c. Crossing table file - file containing the parent crosses to be simulated
   d. Linkage map file - file containing the physical position of each SNP marker in the genotype file

   

4. Click Select GS Model and select an evaluated model.

   

5. Click Select Genotype to upload a Genotype file. The Genotype file should be Phased. If the Genotype file is not Phased, the system will return an error.

   

6. Click Select Crossing Table to upload a Crossing Table file

   

   

7. Click Select Linkage Map to upload a Linkage Map file

   

8. Enter a name for the simulation.

   

9. Click Simulate.

   

10. By default, the initial status will be PROCESSING, which means that the simulation is ongoing.

    

11. You can click the refresh button to see the latest STATUS.

    

12. If the analysis is successful, the STATUS column should be SUCCESS.

    

13. On the Crossing Simulation page, click on the record with SUCCESS status.

    

14. You will be redirected to the simulation's overview page. Details such as Name, Genotype file used, and creation date are displayed. On the same page, click result.

    

15. Click result to view the simulation result.

    

16. You will be redirected to the simulation result. The chart displays the performance of each parent cross in terms of mean and variance.