Using MAPMAKER/EXP

You will need Mapmaker/EXP for this part. If you don't want to use Mapmaker/EXP, then you can use the already prepared files that come with the distribution. Otherwise, ftp to genome.wi.mit.edu and cd to distribution/mapmaker to get the programs. A file sample.raw comes with Mapmaker/EXP.

Each number is a command in a sequence to be done in Mapmaker/EXP. Anything inside of square braces are comments and should not be typed into Mapmaker/EXP. Start up Mapmaker/EXP in an appropriate subdirectory and proceed with these commands:

1. prepare data sample.raw [Input the data from the raw file.]
2. photo sample.tutorial [Save what you do in a log file.]
3. sequence 1 2 3 4 5 6 7 8 9 10 11 12 [Start with all markers.]
4. group [Group them into linkage groups]
5. sequence { 1 2 3 5 7 } [Use randomly ordered group 1 makers.]
6. compare [Compare all orders. For each in turn, calculate the Likelihood.]
7. sequence 1 3 2 5 7 [Decide that this is the best order and specify it.]
8. map [Print the map to the screen. This attaches distances as well.]
9. sequence 4 6 8 9 10 11 12 [Now use the rest of the markers.]
10. list loci [Summarize the number of informative progeny.]
11. lod table [Show pairwise distances and linkage LOD scores.]
12. sequence {8 9 10 11 12} [Use a randomly ordered subset of markers from group 2.]
13. compare [Compare all orders. For each in turn, calculate the Likelihood.]
14. sequence order1 [Use the best order from the compare command.]
15. try 4 6 [Try all possible positions of markers 4 and 6. Also, try unlinked idea.]
16. sequence 4 11 8 12 9 6 10 [This is the best sequence.]
17. make chromosome c1 [Create chromosome 1.]
18. sequence 1 3 2 5 7 [Specify the sequence of markers on chromosome 1.]
19. attach c1 [Attach the sequence to chromosome 1.]
20. framework c1 [Create the framework (puts in distances) for chromosome 2.]
21. make chromosome c2 [Create chromosome 2.]
22. sequence 4 11 8 12 9 6 10 [Specify the sequence of markers on chromosome 2.]
23. attach c2 [Attach the sequence to chromosome 2.]
24. framework c2 [Create the framework (puts in distances) for chromosome 2.]
25. quit [Exit the program. The map will be in sample.maps.]

On a UNIX machine, you will now have a file called sample.maps. On a PC, it will be called sample.map. It will be one of these two on a Macintosh. Rename this output file to sample.mps, and use it along with the sample.raw file for the next part.