Select menu: Stats | QTLs (Linkage/Association) | Data Import/Export | Save Flapjack Project File
Flapjack is a tool for graphical genotyping and haplotype visualization that can routinely handle the large data volumes generated by high throughput SNP and comparable genotyping technologies. Its visualizations are rendered in real-time enabling for rapid navigation and comparisons between lines, markers and chromosomes. Data and results from a QTL analysis in Genstat can be saved into a Flapjack project file that can the be displayed in Flapjack.
To create a Flapjack project file Flapjack must be installed on your system. The genotypic (marker and map) data must be provided and can either be supplied as Genstat data structures or genotypic and map files. Trait and QTL data can optionally be included in the file and can either be supplied as Genstat data structures or text files (see http://bioinf.scri.ac.uk/flapjack/ for the format of the trait and feature files).
If data are stored within the QTL data space then after a QTL analysis is run the genotypic, trait and QTL data tab pages will be automatically filled in. In this situation you would only need to enter details on the Flapjack project tab page before creating the file.
Genstat requires a project file to use the file extension .flapjack to open a project file within Flapjack. If you use another file extension then the project file will only open in Flapjack if you have associated that file extension with Flapjack on your system.
The data and options for creating a project file are displayed on different tabbed pages as follows:
|Flapjack project||Options for saving the project file.|
|Genotypic data||Options for specifying the genotypic (marker and map) data to be included in the project file.|
|Trait data||Options for specifying the trait data to be included in the project file.|
|QTL data||Options for specifying the results from a QTL analysis to be included in the project file.|
|Export files||Options for specifying the files to form the Flapjack project file.|
|Clear||Clear all fields and list boxes.|
|Help||Open the Help topic for this dialog.|