Map block

Between the -start token and the -stop token, you should have a repeating sequence of a -Chromosome token followed by an integer or sting, then markers ordered, with their names followed by the appropriate distances. You should be consistent with the tokens following the -Chromosome token: Either have them all be unique chromosome names or unique integers from 1 to the number of chromosomes indicted with the -chromosomes token.

This example has the markers followed by their positions in centiMorgans. Please give all markers unique names.

-named      yes  
-start 
-Chromosome 1
   Marker1_1    0.0
   Marker1_2   10.2
   Marker1_3   34.1
   Marker1_4   43.3
   Marker1_5   52.1
-Chromosome 2
   Marker2_1    0.0
   Marker2_2   13.7
   Marker2_3   19.1
   Marker2_4   24.8
-stop

In the above, the line Marker1_2 10.2 means that Marker1_2 is on chromosome 1 at position 10.2 cM from the left telomere. If you want to give the chromosomes names, then the above could have been

-named      yes  
-start 
-Chromosome X
   Marker1_1    0.0
   Marker1_2   10.2
   Marker1_3   34.1
   Marker1_4   43.3
   Marker1_5   52.1
-Chromosome First
   Marker2_1    0.0
   Marker2_2   13.7
   Marker2_3   19.1
   Marker2_4   24.8
-stop

If -named had a value of no in the preamble, then the format of the distances would be:

-named     no  
-start 
-Chromosome 1      0.0 10.2 34.1 43.3 52.1
-Chromosome 2      0.0 13.7 19.1 24.8
-stop

That is, the names would be skipped.

You can also create a map where the markers are not on the telomeres. If you are inputting the map based on positions, then

-start 
-Chromosome 1
   Marker1_1    5.0
   Marker1_2   10.2
   Marker1_3   34.1
   Marker1_4   43.3
   Marker1_5   52.1
   Telomere    55.3
-Chromosome 2
   Marker2_1    4.0
   Marker2_2   13.7
   Marker2_3   19.1
   Marker2_4   24.8
   Telomere    27.4
-stop

would mean that there is DNA outside of the first and last markers on a Chromosome. The keyword 'Telomere' is recognized by Rmap as a telomere and not as a marker.

If you are inputting intervals, then the same map would look like

-start 
-Chromosome 1
   Telomere     5.0
   Marker1_1    5.2
   Marker1_2   23.9
   Marker1_3    9.2
   Marker1_4    8.8
   Marker1_5    3.2
-Chromosome 2
   Telomere     4.0
   Marker2_1    9.7
   Marker2_2    5.4
   Marker2_3    4.7
   Marker2_4    2.6
-stop

That is, you need to indicate that the telomeric DNA comes first. These two maps should give the same result when run through Rmap.

WARNING: do not use 'Telomere' as a marker name. This keyword is case sensitive, so 'telomere' is not the same as 'Telomere'.