GMT Tutorial Exercise 23 - Workflow 2 - Step 18

Export the GeneMapper marker data table

• GeneMapper allows to export sample and genotype data with preset and customised formats.
• To ensure that the export format is consistent and compatible with the GENica Marker Tools GEMDB import format, it is a good idea to create a personal, customised table as described here.

1. Select the Genotypes tab on the main GeneMapper window.




2. Select New... from the Table Setting drop-down box on the main GeneMapper window:
   




3. The Table Setting Editor interface opens. On the General tab (see next screenshot), enter a name and choose a security group (if more than one are available) for the new table setting.
   




4. Click on the Genotypes tab (see next screenshot). Tick the columns to be displayed under Show in the Column Settings box of this tab.
   Choose columns to suit your preferences, ensuring that as a minimum, the following fields are included:
   • Sample File
   • Sample Name
   • Marker
   • Dye
   • Allele
   • Run Name
   • Panel

   Note: Including the fields dye, run name and panel is a good idea for future sample tracking: Information about the dye that was used to label a marker is necessary to correct for dye-drift effects. This field is therefore required if data are to be imported to GENica Marker Tools. If entries in fields run name and panel have been left as created by the Automated Designer macro and by the ABI3730 fragment separator, they will be based on entries made for the experiment name, the kit name, and the plate number: Run name: Identical to the name of the folder where *.fsa files are stored; the run name combines the run date, experiment name, kit name and plate number (if applicable) and a run number. Panel name: A combination of a 3-letter abbreviation of the experiment name and the kit name.

   




5. Choose other Genotypes table settings as desired (e.g. number of alleles to be shown, etc.)




6. Click OK to save the new table setting and to close the Table Setting Editor box.




7. Ensure the new table setting is selected from the Table Setting drop down box.




8. In the Genotypes tab of the GeneMapper window, select all the genotype data to be included in the report (use Crtl+A to select all).




9. Select File » Export Table As... from the main GeneMapper menu.




10. Save the exported genotype data in an appropriate place, e.g. the folder that was created for this experiment.
    Note:
    By default, GeneMapper will create a file name that is identical to the project name, followed by "Genotypes Table", for data exported in this way.




11. If desired, this file can be imported directly to GENica Marker Tools, see the instructions for GEMDB»IMPORT.