Using WinQTLCart - a high-level overview

Previous  Top  Next

Your goals in using WinQTLCart may include preparing data for publication or continued research into possible QTL sites.

Step 1—Preparing your source data
Your data files may come from another program or they may exist as raw data files. For WinQTLCart to work with your files, they need to conform to the program's .MCD file format. Review that file, as well as the other files included in the WinQTLCart distribution, such as the .QRT, .QPE, and other files. These are all text files that you can view in any text editor.

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, Creating a new source data file from raw data, Creating simulation data

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, WinQTLCart cannot import Map information from selected file, Invalid file or wrong format messages

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, MCD file format

Step 3—Analyzing data using QTL Mapping Methods
With WinQTLCart able to view the data, you can then select any of six 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, Interval Mapping, Composite Interval Mapping, Multiple Interval Mapping, Bayesian Interval Mapping, Multiple Interval Mapping

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

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, Exporting results from the Graph window, Exporting source data to an MCD file, Exporting source data to QTL Cartographer