QTL Cartographer has the added capability of reading map files generated
by Mapmaker/EXP landeretal@87,lincolnetal@92b.
Genetic marker order and chromosome assignment may be
accomplished using Mapmaker/EXP. Once map order is established,
chromosomes may be saved to external files using the following
Mapmaker/EXP commands (in Mapmaker/EXP):
make chromosome c1
seq M1 M2 M5 M4 M3
A chromosome c1 is defined, and the marker order (for example: M1, M2, M5, M4, M3) assigned. The ``attach'' and ``framework'' commands tell Mapmaker/EXP to save this marker order on chromosome c1. See Section 5.8.1 for a more detailed example of using Mapmaker/EXP to create the genetic linkage map.
After all chromosomes are defined and marker order assigned, exit Mapmaker/EXP. You will find files in your directory with the extensions, ``*.data'', ``*.maps'', ``*.traits'', ``*.xmaps''. The ``*.raw'' file contains the original genotype and phenotype information. The ``*.maps'' file contains the saved marker order per assigned chromosome, as well as the estimated recombination fractions between each marker in the established order. On MS-DOS machines, the extension may be ``*.map'' rather than ``*.maps''. It would be a good idea to rename this file with a ``*.mps'' ending, so as not to confuse QTL Cartographer with its own genetic linkage map file.
The map order, chromosome, and recombination fraction estimate information may be used in QTL Cartographer by specifying ``*.maps'' as the input file for Rmap. The ``*.raw'' file is the input for the Rcross utility.