1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Karst2011_BMMI816xBMMI806_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 markers;


3. For the genotypes of this cross: (cM=centimorgan, bp=basepair)
(1) This propject used SNP markers and all the marker positions were updated in B37, no any missing markers in the B37 data file;

(2) The original file had genotype values of F1, F2 and G3 generation, it only had phenotype values of G3 animals; 

(3) Potential genotype errors have been detected by Rqtl program after data input -- 38 BB genotypes were found from female mice from cross (AxB)x(AxB) on the X chr; 41 AA genotypes were found from female mice from cross (BxA)x(BxA) on the X chr 
(A=BMMI816 strain, B=BMMI806 strain); 


4. For the phenotypes of the cross:
(1) Change the letters in "sex" from f to 0, m to 1 and save the changes in B37 data file; 

(2) Change the letters in "pgm" from a to 0, b to 1 and save the changes in B37 data file; 

(3) Change the missing data in phenotypes from NA to "-" and save the changes in B37 data file; 

(4) The F1 and F2 mouse population didn't have phenotypes in original file, they were excluded from B37 data and B37 data only had the values of G3 animals; 

(5) There were multiple pages in original data file. The phenotype and genotype values of G3 generation were selected and combined into B37 data file, all the original information pages have been kept in description file; 


5. Except the "csv" file mentioned above, I also saved the description file, original data, data with B37 map and data process together as a big excel file ("Data_Description_BMMI816xBMMI806_Karst2011.xlsx") (1st curating work is finished on 7/21/2011). 


6. Information updated on 10/30/2011: 
Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. The markers on chr 2 might have correlations with the markers on chr 6 (observed from RF plot).  All quality control plots were saved in "QCReport_Karst2011.pdf".