The input data format for QTL Cartographer is fairly involved, but it's well documented. If this were a course in QTL analysis, I'd expect you to become fully conversant with the input formats and their meanings. Fortunately for you, I don't expect that at all. For Problem #5, which will involve some QTL analysis, I'll get the data into the right format for you. Still, it's useful to take a brief look at the data format, so you can see the type of data that's involved in a QTL analysis. Download the file realdat_In.mcd from http://darwin.eeb.uconn.edu/eeb348/supplements-2006/Maize.mcd and open it in WinQTLCart. You'll find the following description of the data on your screen:
#FileID 901540162 #bychromosome /* One way to make comment on data source file */ -type position //default is interval -function 1 //default is 1 -Units cM //default is cM -chromosomes 1 -maximum 12 -named yes -start -Chromosome C1 // Another way to comment Mk01_01 0.0000 Mk01_02 37.8000 Mk01_03 49.1000 Mk01_04 59.8000 Mk01_05 62.8000 Mk01_06 86.7000 Mk01_07 92.7000 Mk01_08 108.2000 Mk01_09 112.5000 Mk01_10 134.6000 Mk01_11 140.0000 Mk01_12 149.8000 -stop
There is one chromosome represented in our marker data (labeled c1). The last table gives the name of each marker, in linkage map order, and the distance to the next marker.
The crossing data follows in the next section and is quite a bit more complicated.
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#bycross
-SampleSize 171 //Individual number
-Cross SF2 //default is B1
-traits 1
-missingtrait . //default is . and may use -losttrait
-case yes
-TranslationTable //can omit
AA 2 2 //default 2
Aa 1 1 //default 1
aa 0 0 //default 0
A- 12 12 //default 12
a- 10 10 //default 10
-- -1 -1 //default -1
-start markers
Mk01_01 2 1 1 1 0 1 2 0 1 0 1 2 2 1 1 1 1 2 0 2
0 2 1 1 2 1 0 0 2 2 1 2 1 1 1 0 1 1 1 0
1 2 2 1 2 0 0 0 1 2 1 2 1 1 0 1 0 1 1 0
1 2 2 0 1 1 1 0 1 0 2 1 1 1 2 1 2 2 0 2
0 0 1 1 2 0 1 1 1 1 1 2 1 1 1 2 1 0 1 0
0 2 2 0 1 0 1 2 0 2 1 2 2 2 1 1 2 0 1 0
0 1 1 2 2 0 1 1 1 1 1 2 0 0 0 2 1 0 0 1
1 1 0 2 1 1 1 0 1 1 1 0 1 1 2 1 0 1 1 1
1 2 1 1 1 1 2 1 0 1 2
.
.
.
Mk01_12 0 1 2 2 1 0 2 2 1 0 0 1 1 1 2 1 0 0 1 0
0 0 2 0 1 0 2 1 1 1 2 1 0 1 2 0 2 2 0 1
1 2 1 2 1 1 1 1 1 2 1 0 2 2 1 1 0 1 1 2
2 1 1 1 2 1 0 2 1 1 1 0 2 1 1 0 2 2 2 2
0 1 2 1 1 1 0 1 2 0 1 1 1 2 0 2 0 1 1 2
1 0 2 1 0 1 1 1 1 1 1 1 1 1 0 1 1 2 0 2
2 1 0 1 1 1 1 1 2 0 1 2 1 1 1 0 0 0 1 2
1 2 1 0 2 2 2 1 1 0 1 1 2 1 2 0 0 1 1 1
0 0 2 1 1 2 1 2 1 1 0
-stop markers
-start traits
Trait_1 6.2500 3.0000 3.0000 4.0000 3.0000 3.7500 8.2500 2.5000 4.2500 4.5000 6.0000 3.2500 5.5000 7.2500 5.5000
4.0000 2.7500 7.5000 6.0000 4.7500 2.7500 5.5000 1.7500 5.0000 4.0000 4.0000 2.0000 3.0000 4.7500 3.7500
5.7500 8.0000 3.0000 2.2500 3.5000 6.7500 2.2500 3.5000 6.2500 1.5000 3.5000 4.0000 6.2500 3.0000 7.2500
1.7500 7.2500 1.2500 7.2500 6.7500 6.5000 2.7500 3.5000 4.2500 3.0000 6.2500 1.5000 3.2500 4.7500 2.2500
2.7500 5.0000 3.0000 5.0000 3.2500 6.7500 6.2500 1.2500 2.7500 3.0000 8.2500 3.5000 2.7500 7.2500 5.7500
5.2500 6.7500 6.0000 1.5000 3.5000 5.0000 5.0000 3.7500 4.0000 4.5000 1.5000 7.5000 3.2500 7.5000 2.7500
5.5000 2.5000 3.0000 5.0000 3.0000 2.7500 2.7500 3.5000 7.0000 1.7500 2.7500 3.5000 6.7500 2.7500 3.0000
2.7500 2.7500 5.7500 2.7500 6.5000 1.7500 4.7500 4.7500 3.5000 5.5000 6.5000 5.0000 4.7500 2.2500 2.0000
4.2500 4.2500 6.0000 5.2500 6.0000 3.5000 2.2500 3.0000 4.5000 4.0000 8.2500 4.7500 1.5000 1.2500 2.2500
6.7500 7.5000 2.5000 2.0000 2.5000 2.5000 7.5000 2.0000 4.0000 2.7500 3.0000 3.7500 6.5000 4.2500 3.5000
1.7500 4.0000 5.2500 2.5000 7.2500 2.7500 1.0000 7.5000 4.5000 5.7500 4.5000 4.5000 3.5000 5.5000 1.7500
5.7500 4.0000 3.5000 5.5000 3.0000 5.7500
-stop traits
-quit
-end
After some basic information about the structure of the data the line -start markers denotes the beginning of the marker information. The genotype of the 171 individuals scored is entered following the label form the marker. When the marker data is finished (-stop markers), we start the trait information (-start traits). After a short label describing the trait, the information for each individual is entered.