Flapjack Help

For more information on Flapjack, or to download the application, please visit the Flapjack web site.

Tip

We now have a range of Video Tutorials that you can watch to learn how to use Flapjack.

Getting started

• Quickstart
  • Importing data
  • Browsing the data
  • Interacting with Flapjack

Dealing with data

• Projects & Data Formats
  • Data sets, maps, and genotypes
  • Flapjack views
  • Phenotypes/Traits
  • QTLs
  • Graphs
• GOBii QTL Format
• Pedigree Information
• Favourable Alleles/Alt Marker Names
• Import Data
  • Importing data
  • Advanced data import options
• Duplicate Markers
• Export Data
• Quick Export Data
• Export Image

Visualizing genotypes

• Genotype Visualization
  • Genotype display
  • Chromosome overviews
  • Line information
  • Chromosome display
  • Line and marker overviews
• Modes and Views
  • Navigation mode
  • Marker mode
  • Line mode
• Selecting Lines and Markers
  • Marking selections
  • Selecting monomorphic markers
• Show/Hide Lines
  • Hiding lines
  • Restoring lines
• Show/Hide Markers
  • Hiding markers
  • Restoring markers
• Filtering Markers
  • Filter missing markers
  • Filter missing markers by line
  • Filter heterozygous markers by line
  • Filter monomorphic markers
• Chromosome Map Scaling
  • Global map scaling
  • Local map scaling
  • Classic map scaling
• Colour Schemes
  • Nucleotide model
  • Simple 2 colour model
  • By similarity to line (2 colour)
  • By similarity to marker (2 colour)
  • By allele frequency
  • Random colour schemes
• Customize Colours
• Allele Frequency Threshold
• Bookmarks
  • Creating a bookmark
  • Deleting bookmarks
• Toggle Visible Displays
• Create New View
• Database Link Settings
  • Genotype File Headers

Other visualizations

• Chromosome Visualization
• Phenotype Visualization
  • Importing phenotypic data
  • Phenotype summary information
  • Visualizing alongside genotype data
  • Sorting by phenotype
• Select Traits
• QTL Visualization
  • Importing QTL data
  • QTL summary information
  • Displaying QTLs
  • Interacting with QTLs
  • Filtering visible QTLs
• Filter QTLs
• Graph Visualization
  • Importing graph data
  • Interacting with a graph

Analysis features

• Find by Name
  • Search options
  • Example regular expressions
• Sort Lines
  • By similarity
  • By trait
  • By importing an order
• Similarity Matrix Creation
• Dendrogram Creation
• Marker Assisted Back Crossing
  • MABC QTL format
  • Recurrent parent proportion (RPP) calculations
  • Weighted calculation
  • Unweighted calculation
  • Genome Coverage
  • Linkage Drag(LD) Calculations
• Marker Assisted Back Crossing Tutorial
  • Tutorial data
  • Importing data
  • Exploring and filtering data
  • Running the analysis
  • Viewing the analysis results
  • Filtering the results
  • Sorting the results
  • Selecting within results
  • Ranking results
  • Exporting results
  • Viewing results in the genotype view
  • Conclusion
• Pedigree Verification (F1s Known Parents)
  • Options
  • Understanding the statistics
• Pedigree Verification (F1s Known Parents) Tutorial
  • Importing data
  • Exploring and filtering data
  • Running the analysis
  • Viewing the analysis results
  • Filtering the results
  • Sorting the results
  • Selecting within results
  • Exporting results
  • Viewing results in the genotype view
  • Conclusion
• Pedigree Verification Lines (parental contribution)
• Pedigree Verification - Lines (parental contribution) Tutorial
  • Importing data
  • Exploring and filtering data
  • Running the analysis
  • Viewing the analysis results
  • Filtering the results
  • Sorting the results
  • Selecting within results
  • Exporting results
  • Conclusion
• Forward Breeding
  • Input files
  • Output Statistics
• Indexed Forward Breeding
  • Output statistics
  • Batch analysis results summary
• Analysis Results Tables
  • Selecting lines
  • Auto selecting lines
  • Filtering lines
  • Sorting lines
  • Exporting to a file
  • Ranking lines
  • Don’t sort/filter
• Batch Analysis
  • Launching a batch analysis
  • Working with batch analysis results
  • Exporting data
• Video Tutorials

Miscellaneous topics

• Preferences
  • General
  • Visualization
  • Warnings
• Tips and Shortcuts
• Command Line Support
  • Advanced Options
  • createproject.exe (jhi.flapjack.io.cmd.CreateProject)
  • creatematrix.exe (jhi.flapjack.io.cmd.CreateMatrix)
  • mabcstats.exe (jhi.flapjack.io.cmd.GenerateMabcStats)
  • pedverf1stats.exe (jhi.flapjack.io.cmd.GeneratePedVerF1sStats)
  • createf1.exe (jhi.flapjack.io.cmd.GenerateExpectedF1s)
  • splitproject.exe (jhi.flapjack.io.cmd.SplitProject)
• Allocating Memory
  • Windows & Linux
  • macOS