1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Leiter2009_NODx129_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) Change the symbol of heterozyous genotypes from "h" (original data) to "H" (standard format in data sets of QTL archive) in B37 data file; 

(2) All the markers used in this project are mouse SNP markers;

(3) Unable to find cM positions of 27 markers in this cross from Cox map directly, but the map positions used in original file were already average B37 base pair positions (in Mb), I convert them into cM through Map Converter tool. This type of markers are highlighted with light yellow color and please see description file for the details; 

(4) Some markers are at the same position on chr 1,7,9,15,17 in B37 Cox map; 
 

4. For the phenotypes of the cross:
(1) Change the name of trait "Pedigree" to "pgm" in B37 data file; 

(2) Could not find the definition of trait "Insulitis_Diabetes" from paper directly, the definition in description file is inferred from other phenotypes. In this trait, the value was 5 if the mouse was diabetic, only mouse "WZ00309" was different and the value of it was 4 (it may be phenotyping error);

(3) Could not find the definition of trait "GroupInsulitis_Diabetes" from paper directly, the definition in description file is inferred from other phenotypes. In this trait, the value was 3 if the mouse had diabetes, but the value of diabetic mouse "WZ00185" and "WZ00309" was 2 in data file (they may be phenotyping error); 


5. Except the "csv" file mentioned above, I also saved the description file, original data, data with B37 map, data process and list of missing markers together as a big excel file ("Data_Description_NODx129_Leiter2009.xlsx") (1st curating work is finished in 2009, files are updated on 12/10/2010).


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

(2) Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. The last marker on chr 5 might have a problem. All quality control plots were saved in "QCReport_Leiter2009.pdf".