1. Download the sample data.
  2. Select "New Analysis".

  3. Choose the sample data under the "Trait Set File" field.
  4. Select "2010 Project" under the "Marker Set Id" field.


  5. You will see something like the figure below. Some of the accessions in the trait data could not be matched with accessions in the marker data. Click the red button labelled "NEW (Unmatched genotypes)" to resolve this.


  6. In this screen you can alter the marker set ("Details" tab) and try to find equivalent marker set accessions for the trait set accessions ("Matching genotypes" tab). Trait set accessions without matching marker set accessions will simply be ignored during analysis. Equivalent marker set accessions can be found for the trait set accessions Fäb-2, Fäb-4, Kno-10, Kno-18, Löv-1, Löv-5, Vår2-1 and Vår2-6 from the sample data.
  7. Click the red button labelled "NEW (Submit matched genotypes)" when you are finished matching accessions.

    Match genotypes

  8. Your job should now be running. Wait until it's finished.
  9. Upon completion, you can view which marker associates most strongly with each trait.
  10. There's also a Manhattan plot that provides quick overview of which positions in the genome have the strongest association.