GMT Tutorial Exercise 21 - Workflow 1 - Step 17

Using the macro - the Primer Screening Analyser worksheet

Shown below is the Primer Screening Analyser worksheet of the Automated Designer for Whole Genome Scan macro.
Follow the instructions on this worksheet to import and analyse the GeneMapper report table (generated in the previous step of this workflow) to find markers that are polymorphic for a specified set of DNA samples. Further explanations below.

If required, open the Automated Designer for Whole Genome Scan macro for your experiment and enable macro functions as described previously in this workflow.
Use the Save As... option and re-save the macro without changing its name or location. Click yes at the "file overwrite" warning. This step is required to ensure that macro-generated files are saved in the same directory as the macro.
Use the Next Sheet / Previous Sheet buttons on each worksheet to find the Primer Screening Analyser worksheet shown above.

The macro automatically detects polymorphic markers by comparing the size (in base-pairs) of alleles marked in GeneMapper for each DNA sample in a specified set of DNA samples.
The macro will call a marker polymorphic if the allele sizes for the DNA sample set that is being compared differ by more than one base-pair.
The macro records the allele size range for each marker, calculated from the smallest and largest allele sizes recorded for the marker in the specified set of DNA samples.
If an electrophoretic zone was marked as "m" or "p" according to rule (b) for pre-scoring marker data, the macro automatically calls a monomorphic or polymorphic zone depending on the letter assigned to the left- and right-most peaks bracketing the electrophoretic region.

Click on the Import GeneMapper Table for Sample Plate 1 button.
Browse for the GeneMapper report table created in the previous step of this workflow. This file should have been saved in the same directory as the Automated Designer for Whole Genome Scan macro.
Click Yes at all prompts.
If the experiment required two 96-well ABI sample plates, click on the Import GeneMapper Table for Sample Plate 2 button to import the second report table.

Note:
When two GeneMapper report tables are imported into the macro, both are simultaneously analysed for polymorphic markers.

Select the DNA samples whose pre-scored marker data is to be compared to identify polymorphic markers by entering Yes in the "Compare" column next to samples that are to be included in the comparison.
Two or more DNA samples can be compared, and it is not necessary to include all the available DNA samples.

This starts the comparison. When more than one report table is imported into the macro, both report tables are simultaneously analysed for polymorphic markers.

Upon completing the data analysis, the macro will display the Polymorphism Summary worksheet, see the next step in this workflow.