The default file formats for the three files required for the QTL Applet are now described (generic).
The genotype file should be named filename.gen, the marker file should be named filename.mrk and the trait file named filename.tra (where filename is the name of your file). When (if) the file dialog box appears then select the filename.gen file for opening.
The genotype file format is shown on the left below, the first row contains three numbers representing the number of individuals, (n_ind) the number of markers (n_mrk) and the number of traits (n_tra). Then follows n_ind rows of individuals (lines), each row containing the genotype at each marker locus of the individual. The genotypes are coded 1 homozygous for parent 1, 2 heterozygous, 3 homozygous for parent 2 and 4 missing data. The data can be delimited by tab characters, spaces or commas.
The marker file format is shown below centre. The first column contains the marker names. The second column contains the marker link groups denoted by an integer number starting at 1. The third column contains the respective marker positions.
The trait file format is shown on the right below. Each column represents a single trait, containing all trait values for all n_ind individuals. Clearly in this example, there is only one trait.
Alternate file formats can be chosen through the 'File Format' dialog box, below-left is an example of this with the MapMaker format selected. When a particular format is selected the default genotype coding is inserted into the text boxes, these can be altered as required. Below-right is the identical genotype data to that shown above in the default (generic) format now in MapMaker format. As seen in the file format dialog the JoinMap format is also supported. At present it is still necessary to define the population model (F2, doubled haploid etc) and mapping function (default Haldane) in the Java program.
There is the additional option of specifying the orientation of your data files, this applys to the generic genotype file OR the trait file (which is strictly generic anyway). Thus the data in the genotype file, which by default is individuals (lines) as rows ( = markers as columns) can be specified as being in the lines as columns format. Marker names can also be included although at present they are not used (in the future an option to sort genotype data may be added). In the default format marker names should head the columns, in the alternate format a marker name will be at the start of each row. The same procedure applys to trait file formats.
At present, UNIX users are advised to use lowercase letters for their directory & file names when using this software.