1. The original data had several separated data sets --- pheno.dat, geno.dat, markerpos.txt, mnames.txt and pnames.txt. Combine them as a standard CSV cross file like others in QTL archive, update the map with Build37 Cox genetic map (BC_B37) and save the new file as "Kim2001_B6xTH_BC_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 TH allele from "1" to "T", heterozygous allele from "0" to "H", missing genotypes from "9" (original data) to "-" (standard format in data sets of QTL archive) and save the changes in B37 data file; 

(2) Marker "D2Mit17" and "D15Mit228" miss 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 BC_B37 bp position of this marker currently (this type of markers is highlighted with rose color in description file);

(3) Marker "D8Mit339", "D12Mit233" and "D19Mit10" miss bp positions in Cox genetic map, assign the positions from current MGI database. (this type of markers are highlighted with gold color in description file);

(4) Marker "D15Nds2" is unmapped in Cox map. To get bp position, primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR. Next, convert the bp into cM through Map Converter tool in CGD website (http://cgd.jax.org/mousemapconverter/) (this type of markers are highlighted with tan color in description file);

(5) Marker "D15Mit220" 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);

(6) Marker "D17Mit54" is unmapped in Cox genetic map, the primer sequences could not be found in MGI, either. Use interpolating algorithm in Rqtl to calculate the B37 cM position, the bp information of them are unavailable (this type of markers is highlighted with lavender color and please see the description file for details);

(7) Some markers are at the same position (cM) on chr 6 in B37 Cox map; 


4. For the phenotypes of the cross:
(1) The original data didn't have "mouseID", add a column of "Mouse Num" in B37 data file; 

(2) Change the symbol of missing phenotypes from "-999" to "-" and save the changes in B37 data file; 

(3) Correct the errors of two mice in trait "Insulin" and save the changes in B37 data file; 

(4) The publication included two backcrosses and this is the data of backcross between TH (TallyHo) and C57BL/6J; 


5. Except the "csv" file mentioned above, I also saved the description file, original data files, data with B37 map, data process and list of missing markers together as a big excel file ("Data_Description_B6xTH_BC_Kim2001.xlsx") (1st curating work is finished on 9/23/2011). 


6. Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. The 1st marker on chr 5 might have a problem (observed from map comparison plot). All quality control plots were saved in "QCReport_Kim2001.pdf".