Select menu: Stats | QTLs (Linkage/Association) | Data Import/Export | Save Flapjack Project File
This specifies options and settings for exporting data to a Flapjack project file format.
- From the menu select
Stats | QTLs (Linkage/Association) | Data Import/Export | Save Flapjack Project File.
- On the Flapjack project tab, set options as required then click OK.
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 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:
|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.|
Provides a space to specify the Flapjack project filename. If the file contains the extension .flapjack the project can be automatically opened within Flapjack. You can browse for a filename by clicking on the button.
Create project using
This option specifies whether the project is to be formed using Genstat data structures or existing files.
Open project in Flapjack
Genstat uses the Flapjack file association to open a project file in Flapjack. When selected if the project filename includes the file extension .flapjack the project will be opened in Flapjack. If the project filename does not include the file extension .flapjack this option will be disabled.
|Location of flapjack||This specifies the folder containing the Flapjack executables. If this field is left blank then Genstat will search the default locations C:\Program Files\Flapjack or C:\Program Files (x86)\Flapjack. You can browse for the folder location by clicking on the button.|
|Display decimal mark using||This specifies how the decimal symbol is to be displayed in Flapjack. The setting Dot (.) will use the UK/US style with a dot, for example 3.23. Alternatively the setting Default language setting will base this on the current Windows language settings.|