1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Mrug2005_B6xCAST_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) Marker "D2Mit51" and "D8Mit259" miss bp positions in both Cox map and MGI. Primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (this type of markers is highlighted with lime color in description file and please see description file for details);
 
(2) Marker "D8Mit14" is missing bp positions in both Cox map and MGI. 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 (this type of markers is highlighted with rose color in description file and please see description file for details);

(3) Marker "D10Mit264" is missing bp position in both Cox map and MGI. The primer sequences found in MGI, but no target templates is found in primer-BLAST in NCBI. We could not identify the B37 bp position of this markers currently (this type of markers is highlighted with dark yellow color in description file);

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


4. For the phenotypes of the cross:
(1) The direction of the cross is not found in paper (highlight in turquoise color in description file);

(2) Could not find the definitions of phenotype "1mother", "mean_logB", "mean_logBP", "mean_logT", "mean_logTP", "mean_logT2BP" and "Prin2" from paper (highlight in turquoise color in description file);

(2) The intervention (type of diet) is missing in paper (highlight in turquoise color in description file);

(3) One mouse (mouse id = 1909) is missing sex information in original file. Set it as missing in B37 data file;  


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_B6xCAST_Mrug2005.xlsx") (1st curating work is finished on 6/30/2011).

6. 5/11/2012: 
Quality control plots (genetic map, missing genotypes plot, map comparision plot and whole genome RF plot) performed and no issues found. All quality control plots were saved in "QCReport_Mrug2005.pdf".