Windows QTL Cartographer 2.5 - FTP Directory Listing

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© 2010 N.C. State University, Bioinformatics Research Center
Using WinQTL - a high-level overview 3
Or, you may not have any data files or any data ready for import. You may instead want to use
WinQTLCart to create simulation data to try out some hypotheses to view potential results.
See these topics for more information: MCD file format 39 , Creating a new source data file from raw
data 44 , Creating simulation data 51
Step 2—Bringing data into WinQTLCart
WinQTLCart can import map and cross data files from MapMaker/QTL, QTL Cartographer, and Microsoft
Excel. As part of the import, WinQTLCart runs verification checks against the data. If the data does not
conform to the accepted format, WinQTLCart displays an error message that should indicate the source
of the problem.
See these topics for more information: Importing files 25 , WinQTLCart cannot import Map information
from selected file 86 , Invalid file or wrong format messages 86
Your source data may not have come from another program, but may instead exist as raw source files.
In that case, using WinQTLCart's Create a New Source File command steps you through all of the steps
needed to translate the raw data into a readable form. The new source file will conform to WinQTLCart's
MCD file format.
See these topics for more information: Creating a new source data file from raw data 44 , MCD file
format 39
Step 3—Analyzing data using QTL Mapping Methods
With WinQTLCart able to view the data, you can then select any of seven different analysis methods.
The end result for some of these methods is another MCD file, but in most cases the process will create
a .QRT result file that WinQTLCart can use to graph QTL information.
See these topics for more information: Single-marker analysis 55 , Interval Mapping 58 , Composite
Interval Mapping 60 , Multiple Interval Mapping 63 , Bayesian Interval Mapping 76 , Multiple-trait
Analysis 63 , Multiple-trait MIM.
Step 4—Viewing results and graphs
WinQTLCart can present your data in graphics suitable for publication. You can show all chromosomes
and their intervals in one display, while the Graph window display offers many parameters to help you
fine-tune the visualization.
See these topics for more information: Drawing a chromosome tree , Graph Window tour
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Step 5—Saving and exporting results
You can save your source data in .MCD format and your results files in .QRT format so you can work
with them later in WinQTLCart. You can also export your results to other selected formats.
See these topics for more information: Exporting source data and results 29 , Exporting results from the
Graph window 31 , Exporting source data to an MCD file 30 , Exporting source data to QTL Cartographer
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