questions for analysis QTL using QTL cartographer

[van charles]

Hi All,
I am using QTL Cartographer to analysis some datasets.  I got 3 datasets from my boss, one is the mapmaker file 'truemap.maps' and the others are the original raw files, 'allmarkers.raw' and 'subsetmarkers.raw'.  They are the same datasets and only difference is the former one contain all the genetic markers which are constant as the 'truemap.maps' and the later one only have the have markers.

Boss requested me to use the map file she gave me (i.e., translate using QTL-Cartographer), and analyze both datasets.  Thus, I am wondering is that possible for me using the map file to analyze the 'subsetmarker.raw' without use Emap to make a new map file.  If possible, what should I do?
Thanks a lot!
Charles