Using the MAPMAKER files

Create a new working subdirectory called mm in your qwork subdirectory. Copy the files sample.mps and sample.raw into it. The former is a genetic linkage map created by Mapmaker/EXP. The latter is Mapmaker/QTL raw file. You will now translate the data files into the QTL Cartographer format, and then analyze the data.

1. Start up Rmap. Select the option to change the filename stem. Change the filename stem to ``sample'' and set the proper working subdirectory. Then select the input file option and change it to sample.mps. Then go ahead with the analysis. Look at the output (sample.map).
2. Start up Rcross. Select the input file option and change it to sample.raw. Then go ahead with the analysis. Look at the output (sample.cro).
3. Proceed with the analysis programs as in the previous examples. Run Qstats, LRmapqtl, SRmapqtl and Zmapqtl. Look at the output after each run.
4. Start up Preplot. Don't change any parameters: Go ahead with the program.
5. View the results usingGnuplot.
6. Start up Eqtl. Go ahead with the analysis. Look at the output (sample.eqt).

The sample files should be in the usual place (QTLCartUnix/example). The UNIX equivalents of the above are

% cd qwork
% mkdir mm
% cd mm
% cp ~/QTLCartUnix/example/sample.* .
% Rmap -A -i sample.mps -X sample
% Rcross -A -i sample.raw
% Qstats -A  
% LRmapqtl -A
% SRmapqtl -A 
% Zmapqtl -A 
% Zmapqtl -A -M 6
% Preplot -A
% gnuplot sample.plt
% Eqtl -A