In this tutorial we will illustrate the use of many of MAPMAKER's features while analyzing a real data set. We have provided these data sets with the MAPMAKER software, and we strongly encourage you to follow along with this tutorial on your computer.
When MAPMAKER starts running, you will first see its start-up banner and a prompt "1>" for the first command. Precisely how you should start MAPMAKER depends on your computer. These issues are described in detail in the "Installation Guide" included with this manual.
Note that throughout this tutorial, we indicate command you type into MAPMAKER in bold italics, while MAPMAKER output is presented in regular type. Throughout this manual, we use the names MAPMAKER and MAPMAKER/QTL interchangeably.
The first step in almost every MAPMAKER session is to load a data file for analysis. If you are starting out an analysis on a new data set, or if you have modified the raw data in an existing data set, you will do this using MAPMAKER's "prepare data" command, as described in the "Data Preparation Guide" , included with MAPMAKER. If instead you are resuming an analysis of a particular (unmodified) data set, you may use the "load data" command, which preserves many of the results from your previous session. Because we are just starting out, we use MAPMAKER's "prepare data" command to load our sample file "sample.raw".
From this file MAPMAKER extracts:
The genotype for each marker in each individual (if available)
Other information may be present in the data files, such as quantitative trait data and pre-computed linkage results. These issues will be addressed later.
Before performing any analyses of our data set, we now instruct MAPMAKER to save a transcript of this session in a text file for later reference. Using the "photo" command, we start a transcript named "tutorial.out". Note that if the file already exists, MAPMAKER appends new output to this file.
************************************************************************ * Output from: * * * * MAPMAKER/EXP * * (version 3.0b) * * * ************************************************************************Type 'help' for help. Type 'about' for general information.
1> prepare data sample.raw preparing data from 'sample.raw'... F2 intercross data (333 individuals, 12 loci)... ok saving genotype data in file 'sample.data'... ok