Windows QTL Cartographer 2.5 - FTP Directory Listing

Contents
WinQTLCart Procedures 25
Setting ................................................................................................................................... the working directory
25
Importing ................................................................................................................................... and exporting
25
Importing files .......................................................................................................................................................... 25
Exporting source .......................................................................................................................................................... data and results
29
Exporting source ......................................................................................................................................................... data to QTL Cartographer
30
Exporting source ......................................................................................................................................................... data to an MCD file
30
Exporting results ......................................................................................................................................................... from the Graph w indow
31
Working ................................................................................................................................... with source data files
31
Opening source .......................................................................................................................................................... data files
32
Working w ith .......................................................................................................................................................... a source file's marker genotype data
32
Working w ith .......................................................................................................................................................... a source file's traits values
33
Working w ith .......................................................................................................................................................... a source file's basic information
34
Working w ith .......................................................................................................................................................... source file's individual information
35
Working w ith .......................................................................................................................................................... source file's chromosome information
37
Working w ith .......................................................................................................................................................... source file's trait information
38
Working w ith .......................................................................................................................................................... source file's other trait information
39
MCD file format .......................................................................................................................................................... 39
Creating ................................................................................................................................... a new source data file from raw data
44
Creating ................................................................................................................................... simulation data
51
Single-marker ................................................................................................................................... analysis
55
Setting ................................................................................................................................... threshold levels (IM & CIM)
56
Setting threshold .......................................................................................................................................................... levels manually
57
Setting threshold .......................................................................................................................................................... levels via permutations
57
Interval ................................................................................................................................... Mapping
58
Running interval .......................................................................................................................................................... mapping analysis
58
Composite ................................................................................................................................... Interval Mapping
60
Running composite .......................................................................................................................................................... interval mapping analysis
60
Multiple ................................................................................................................................... Interval Mapping
63
About the MIM .......................................................................................................................................................... form
63
Creating MIM .......................................................................................................................................................... initial model
65
Regression ......................................................................................................................................................... options
66
CIM search ......................................................................................................................................................... option
68
MIM search ......................................................................................................................................................... option
69
Refining the MIM .......................................................................................................................................................... model
70
Multiple-trait ................................................................................................................................... MIM
72
About the Mt-MIM .......................................................................................................................................................... form
72
Mt-MIM Control .......................................................................................................................................................... File
74
Mt-MIM Functions .......................................................................................................................................................... 75
Bayesian ................................................................................................................................... Interval Mapping
76
Running Bayesian .......................................................................................................................................................... interval mapping analysis
77
Multiple-trait ................................................................................................................................... analysis
78
Drawing ................................................................................................................................... a chromosome tree
78
Adding QTL positions .......................................................................................................................................................... to the chromosome graphics
80
Tutorials 81
Import ................................................................................................................................... data files
81
© 2010 N.C. State University, Bioinformatics Research Center
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