1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Peters2004_C3HxCAST_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 CAST strain allele from "0" to "T", C3H strain allele from "2" to "C", heterozygous allele from "1" to "H", missing genotypes from "=" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 

(2) The bp position of marker "D2Mit190" is missing in both Cox map and MGI. Primer sequences found in MGI, but no target result is found in primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently (the letters are highlighted with brown color in description file); 

(3) Marker "D3Mit352" misses 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 (it is highlighted with green color in description file); 

(4) Marker "D13Mit256" misses bp position in both Cox map and MGI database. No primer sequences are available from MGI. We could not identify the B37 bp position for this marker currently (it is highlighted with blue color in description file); 

(5) Could not find the positions of marker "B-Spectrin" in Cox map, we found it was "spectrin beta 1" (a protein coding gene) from paper. Assign the bp positions of the gene from MGI, then convert it to cM through Map Converter tool (this marker is highlighted with light yellow color in description file);

(6) 3 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 the details; 

(7) Detect potential genotyping errors by Rqtl after data input -- 2 male mice had 4 heterozygote genotypes on the X chromosome in this cross; 

(8) This project might be a reciprocal F2 intercross, but the direction of the cross and the information of pgm (paternal grandma) were missing in the paper. The "pgm" can be inferred by the R/qtl program but it could be probably poorly; 					


4. For the phenotypes of the cross:
(1) Change the symbol of female mouse in "sex" trait from "F" to "0", male mouse from "M" to "1" in B37 data file;

(2) According to the genotypes of the X chromosome, this cross should be a reciprocal F2 intercross, but the information of the cross direction ("pgm"--paternal grandma, which indicates the direction of cross) is not provided in original file and could not be found in the publication. Users can use Rqtl or other program to infer the "pgm" but it is probably poorly; 


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_C3HxCAST_Peters2004.xlsx") (1st curating work is finished in 2009, files are updated on 1/12/2011).


6. 6.  Information were updated on 5/11/2012:
(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 4,7,11,14,16 and 19. Chr 4 and 12 had correlated markers. All quality control plots were saved in "QCReport_Peters2004.pdf".