1. Update the map of the data set with Build37 Cox genetic map (B37) and save the new file as "Farmer2001_C3HxB6_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 the missing genotypes from "" (original data) to "-" (standard format in data sets of QTL archive) and save the changes in B37 data file; 

(2) Marker "D2Mit266" and "D12Nds2" were unmapped in Cox genetic map. Their bp positions assigned based on MGI, then convert them into cM through Map Converter tool (this type of markers is highlighted with light yellow color in description file); 

(3) Marker "D3Mit19" missed 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);

(4) Marker "D14Mit203" missed bp positions in both Cox map and MGI. Primer sequences found in MGI, but no target templates were found in 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);

(5) Marker "D17Nds3" was 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 (this type of markers is highlighted with tan color in description file);

(6) 5 markers missed bp positions in Cox genetic map, assigned the positions from current MGI database. This type of markers are highlighted with gold color and please see description file for details; 

(7) Potential genotype errors have been detected by Rqtl program after data input: 
    34 male heterozygote genotypes were found on the X chromosome;
    17 BB genotypes were found from females from cross (CxB)x(CxB) on the X chromosome;
     6 CC genotypes were found from females from cross (BxC)x(BxC) on the X chromosome;


4. For the phenotypes of the cross:
(1) The definitions of half phenotypes were found in a previous paper "Heritable Susceptibility for Colitis in Mice Induced by IL-10 Deficiency" Bristol, I. J., Cong, Y., Far mer, M. A., Zheng, X. X., Strom, T. B., Elson, C. O.,Sundberg, J. P. & Leiter, E. H. (2000) Inf lamm. Bowel Dis. 6, 290 Ð302;

(2) The definitions of trait "IFNg", "gdTcells" and "B220xIgM" are not found in paper (highlight in blue color);

(3) Trait "Cross" in original file indicated the direction of the cross. Change the name of "Cross" to "pgm" and save the change in in B37 data file ("pgm" is a default parameter in Rqtl to help the program check the genotypes on X chromosome);

(4) Add trait "mouseID" with sequential numbers (1-411) 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_C3HxB6_Farmer2001.xlsx") (1st curating work is finished on 3/30/2011).


6. Information updated on 10/18/2011: 
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 1 might not belong to this chromosome. Chr 8, 9, 13, 15 and 16 had marker order problems. All quality control plots were saved in "QCReport_Farmer2001.pdf".