Whitehead Institute
Constructing Genetic Linkage Maps with MAPMAKER/EXP Version 3.0:
A Tutorial and Reference Manual
Stephen E. Lincoln, Mark J. Daly, and Eric S. Lander
A Whitehead Institute for Biomedical
Research Technical Report
Third Edition, January, 1993
(Beta Distribution 3B)
All MAPMAKER Software and Documentation is (c) Copyright 1987-1993,
Whitehead Institute for Biomedical Research. All Rights Reserved.
All software and documentation is provided without warranty of any kind.
See the included license agreement for details.
Please address all correspondence to:
MAPMAKER Internet: mapmaker@genome.wi.mit.edu
c/o Dr. Eric Lander Bitnet: mapm@mitwibr
Whitehead Institute FAX: 617-258-6505
9 Cambridge Center
Cambridge, MA 02142 USA
Constructing Genetic Linkage Maps with MAPMAKER:
A Tutorial and Reference Manual
Table of Contents:
I. Command Index 2
II. Quick Reference Sheet 4
III. Tutorial for MAPMAKER/EXP Version 3.0
Starting MAPMAKER 6
Finding Linkage Groups by Two-Point Linkage 8
Exploring Map Orders by Hand 10
Displaying a Genetic Map 12
Mapping a Slightly Larger Group 14
Dealing with Larger Data Sets 20
Finding Chromosome Assignments 22
Automatically Finding Map Orders 26
Verifying a Map Order 32
Analyzing Another Chromosome 34
Automatic Error Detection 38
Saving and Drawing Information about a Mapped Chromosome 40
IV. MAPMAKER/EXP Version 3.0 Reference Manual 48
General Information
Basic MAPMAKER/EXP Commands
Sequence Command and Related Features
Two-Point Analysis Commands
Multipoint Analysis Commands
Genome Analysis Features
Systematic Error Detection Mechanism
Three-Point Analysis Mechanism
Joining Haplotypes in Large Data Sets
Parameters and Options
Miscellaneous Commands
Page 2: T.O.C. 1
Page 3: T.O.C. 2
Page 4: QuickRef 1
Page 5: QuickRef 2
Starting MAPMAKER/EXP
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提示符 "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 type of cross, number of markers, and number of scored progeny
The genotype for each marker in each individual (if available) reference group
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
2> photo tutorial.out
'photo' is on: file is 'tutorial.out'
Finding Linkage Groups by Two-Point Linkage

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