Windows QTL Cartographer 2.5 - FTP Directory Listing

6. Select one or all chromosomes to include in the analysis.
© 2010 N.C. State University, Bioinformatics Research Center
WinQTLCart Procedures 63
7. Select one or all traits to include in the analysis. The Traits you select may change the value of
the Threshold controls on the right side of the form.
8. Set the threshold level via either manual input or permutations. For more information, see Setting
threshold levels (IM & CIM) 56
.
9. Click Start to begin QTL mapping analysis. WinQTLCart will open a Save As dialog for you to
save the result file that will be created.
10. If you selected Set control markers manually in step 4b, then WinQTLCart will display the
Select CIM Control Markers dialog box. Enter or edit the marker numbers you want to using the
text box; separate each number with a space. Click on the marker row's cells to toggle their
display in the text box.
When the analysis is complete
WinQTLCart will
Create a QTL mapping result file (*.QRT) and open it in the Graph window
Create a QTL summary information file using the EQTL function.
Display a confirmation box asking if you want to display QTL summary information in the Main
window's Data pane.
Multiple Interval Mapping
What it is
Multiple interval mapping (MIM) uses multiple marker intervals simultaneously to fit multiple putative QTL
directly in the model for mapping QTL. The MIM model is based on Cockerham's model for interpreting
genetic parameters and the method of maximum likelihood for estimating genetic parameters. MIM is
well suited to the identification and estimation of genetic architecture parameters, including the number,
genomic positions, effects and interactions of significant QTL and their contribution to the genetic
variance.
High-level process
Here's a quick overview of how to use WinQTLCart's MIM implementation:
About the MIM form
1. Select the MIM analysis method.
2. Pick a trait you want to work with. (MIM works with only one trait at a time.)
3. Decide if you want to create a model using WinQTLCart's default search procedures or an
alternative (such as Forward, Backward, or CIM).
4. Run the analysis to generate the model.
5. Refine the model as needed by editing individual cells in the model, adding or deleting QTL,
searching and testing QTLs or epistatics, and re-estimating. This part of the analysis can
iterate for as long as you want to search for QTLs.
6. Save the model as a .MDS file (or as a result file using the Refine Model function).
From the Source Data form, open a source data file and select Multiple Interval Mapping as the analysis
method. If there is more than one trait in the dataset, the Select Trait for MIM Analysis dialog appears.
Select a trait from the drop down list and Click MIM... button to open MIM form.