1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Broman2006_B6xC3_B37_Data.csv". This file is ready to be read into Rqtl; 


2. Generate a description file of the project, it includes the general information, definitions of the phenotypes, description of the genotypes and information of the missing markers;


3. For the genotypes of this cross: (cM=centimorgan, bp=basepair)
(1) The data file of this project has 1068 mice in total. The genetic markers in original file was neither DMit nor SNP markers, then the author changed them and used revised marker names with build37 bp positions in his revised file;

(2) Convert all Mbp positions provided by Karl (first author) into sex-averaged cM by using mouse map converter tool, then save these changes (with revised marker names and cM positions) in "Broman2006_B6xC3_B37_Data.csv";

(3) There are 121 markers in original file. Among them, marker "WILSET621151" is omitted by author as they couldn't obtain build37 coordinates. Drop this marker from B37 data file.


4. For the phenotypes, the information of intervention (diet) and mouse age at testing are not found in paper;


5. Add a new reference paper in description file of the project (update on 4/8/2010)
Owens SE, Broman KW, Wiltshire T, Elmore JB, Bradley KM, Smith JR, Southard-Smith EM (2005) 
Genome-wide linkage identifies novel modifier loci of aganglionosis in the Sox10Dom model of Hirschsprung disease. Hum Mol Genet 14:1549-1558


6. Except the "csv" file mentioned above, I also save the description file, original data, data with B37 map and data process together as a big excel file ("Data_Description_B6xC3_Broman2006.xlsx") (1st curating work is finished on 6/23/2009, files are updated on 6/30/2009, 4/9, 10/20, 10/26/2010).


7. Information updated on 10/11/2011: 
(1) Change the name of the map (from "Shifman" to "Cox" map) in description and readme file, add a map reference in description file; 

(2) Change the symbol of female mouse from "F" to "0", male mouse from "M" to "1" and save the changes in B37 data file; 

(3) Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. Chr 11 and 15 had correlated markers. All quality control plots were saved in "QCReport_Broman2006.pdf".