How to request for parental purity analysis?

Owned by Rica Aicel Mariano
Last updated: Dec 06, 2024
3 min read
parental purity analysis.png

 

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To ensure that cross combinations produce the expected genotype, parental purity analysis is done. As such, genotyping data with this specific purpose can now be used to request for parental purity analysis via the Molecular Data Analysis (MDA) tool. Take note that all genotyping data found on the MDA data browser are sourced from the Request manager tool.

Request for purity testing by internal consensus

Once logged in to the Breeding Analytics domain, open the left navigation menu and select the Molecular Data Analysis tool.

Contact a data manager or send a support ticket if log in problems are encountered.

 

  1. Open a genotyping dataset with the purpose “Parental Purity Testing” by clicking the view icon.

image-20241010-032129.png

 

  1. Click the Request Analysis button on the upper right corner of the screen.

If the Request Analysis button is not available, it is because there are no genotype data displayed on the Genotype Data tab data browser. Adjust the default call rate thresholds to display the excluded data.

 

  1. Select Purity testing by internal consensus > Next.

The option to select purity testing by external match will be enabled soon.

 

View and download results for purity testing by internal consensus

As soon as the request is placed, analysis results are immediately available for viewing.

 

  1. Click the Results tab. The data browser shows a result of either TRUE or FALSE will be shown, where:

    • TRUE indicates that all markers matched the expected genotype, and

    • FALSE indicates that at least one marker did not match the expected genotype.

 

  1. On the toolbar, provide a preferred file name on the text field or use the auto-generated one. Click the Download icon to start the download process.

 

  1. A zipped file is exported containing the CSV file of the results.

 

View and download statistics for purity testing by internal consensus

  1. Click the Statistics tab. The data browser shows results for the following:

    • Allele 1 and 2: This provides the count of the most common and second common allele, and

    • Heterozygous and missing: This provides the call count of heterozygous and missing data.

 

  1. On the toolbar, provide a preferred file name on the text field or use the auto-generated one. Click the Download icon to start the download process.

 

  1. A zipped file is exported containing the CSV file of the statistics.

Great! You have successfully requested parental purity analysis for your genotype data!