GMT Tutorial Exercise 5

Import a GeneMapper *.txt file into GEMDB

1. Select GEMDB and then select IMPORT. A screenshot of the GEMDB»IMPORT interface is shown below.
2. Create a new MRT Marker Set for "missing" markers (i.e. markers whose names are not in the MRT Markers wheat and barley database).
   1. Click Add Marker Set. This opens a new screen.
   2. Choose a User Group (e.g. "ARM demo"), enter a Marker Set Name (e.g. "your name non MRT markers"; only use letters, spaces and numbers) and leave Access set to "Private".
   3. Select Save to return to GEMDB»IMPORT.
3. Choose the new marker set from the MRT Marker Set for "missing" markers drop-down box.
4. Select the Project / Group under which to store the data to be imported: "your name_demo", created in Exercise 4.
5. Click on Browse and select the file to be imported ("GEMDB_import_example.txt", downloaded in Exercise 3).
6. Select the Platform Used e.g. ABI 3730 (optional).
7. Do not Convert all '?' alleles to 0 (null) alleles by selecting "No". Only choose "Yes" if question marks were used to identify null alleles, this is not applicable for the demo file. Find out more in the GMT manual...
8. Select "Yes" for Multiplex Ready Technology, if applicable, e.g. for the demo file. Find out more in the GMT manual...
9. Select "barley (4513 : Hordeum vulgare)" from the Species drop-down box.
10. Run Name and Panel Name do not need to be entered if these fields are included in your GeneMapper export file. The demo file you are using in this tutorial includes these fields. The Run Name is automatically created by GeneMapper when *.fsa files are "appended" to a "GeneMapper project". The Panel Name is added to in GeneMapper when samples are analysed.
11. Click Import.
12. Either wait for the import results, or retrieve them via the ADMIN»DASHBOARD "System Messages" box at a later time.
13. A table will appear that details the data that has been imported.
14. Click Finished. The "GEMDB»BROWSE" interface opens automatically, where imported data can be reviewed, see Exercise 6.

The GEMDB»IMPORT interface