1. Update the map of data set with Build37 Cox genetic map and save the new file as "Dorward2005_SWXJxCAST_B37_Data.csv". The file is ready to be input into Rqtl;


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


3. For the genotypes of this cross: (cM=centimorgan, bp=basepair)
(1) Change the symbol of genotypes from "0" (allele of SWXJ in original data) to "S", "1" (heterozygous allele in original data) to "H" (standard format in data sets of QTL archive) and save the changes in B37 data file; 

(2) Three markers miss their bp positions in Cox genetic map, assign the positions from current MGI database. This type of markers are highlighted with orange color and please see description file for details;

(3) Marker "D3MIT352" and "D19MIT6" miss bp position in both Cox map and MGI database. Primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (they are highlighted with green color in description file); 

(4) Marker "D14MIT160" and "DXMit231" miss bp position in both Cox map and MGI database. Primer sequences found in MGI, but their locations don't match the result from primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently (these markers are highlighted with pink color in description file);


4. Don't detect any problems in phenotypes of the cross;


5. Except the "csv" file mentioned above, save the description file, original data, data with B37 map, data process record and missing marker list together as a big excel file ("Data_Description_SWXJxCAST_Dorward2005.xlsx"). (first curating work finished at 5/26/2009, files updated on 7/1/2009, 10/26/2010)


6. Information updated on 10/18/2011: 
(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) Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. Problematic markers were found on chr 2, 4 and 6. All quality control plots were saved in "QCReport_Dorward2005.pdf".