1. The original data file (TarantinoCross_060807.csv) has SNP markers, but they are not RS or JAX markers we always use. The only information I can use is the Mb positions of genotypes are based on Build 33. I copy the positions into the Lift Genome Annotations database (UCSC) and convert them into the Build 37 positions. Except one marker ("4.154.007"), the rest are converted successfully; 

  
2. Couldn't find the new positions of marker "4.154.007" (154.7 Mb in B33) in build 37. The information from "hgLiftOver" tool showed this sequence was deleted and we don't have the information of primer pairs. We use the interpolating algorithm in Rqtl to calculate the new cM position in B37 data file;

    
3. Convert and update the map of data set with Build37 Cox genetic map (cM) and save the new file as "Bailey2008_B6xC58J_B37_Data.csv". The file is ready to be read into Rqtl; 


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


5. For the genotypes of this cross: (cM=centimorgan, bp=basepair)
(1) Change the symbol of missing genotypes from "O" (original data) to "-" (standard format of data sets in QTL archive) in B37 data file; 

(2) The new position of marker "4.154.007" is calculated by the interpolating algorithm in Rqtl (see the information above) , the bp information is unavailable; 

(3) Detect potential genotyping errors by Rqtl after data input:
    59 male mice had heterozygote genotype "BC" on the X chromosome in this (BxC)x(BxC) cross;
    39 female mice had "CC" genotypes on X chromsome in this (BxC)x(BxC) cross;

(3) The map comparsion plot and recombination fractions plot of this project are ok; 


6. For the phenotypes of the cross:
(1) Do not find the unit of "ACTFACT" and "ANXFACT" in paper;

(2) Do not find the exact definition of "PCTT10" in publication, I think this phenotype is "Percent time spent in center of arena (interval of 10 min)" based on the information provided by paper;

(3) Change PGM from "B" into number "0" in the B37 data file (the direction of the cross is (B6xC)F1 x (B6xC)F1);
 

7. 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_B6xC58J_Bailey2008.xlsx") (The 1st curation is finished on 10/5/2009, files updated on 10/20, 10/26, 11/17/2010).


8. Information were updated on 9/28/2011:
(1) Change the name of the map (from "Shifman" to "Cox" map) in readme file, add a map reference in description file (information were updated on 9/28/2011). 

(2) 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_Bailey2008.pdf".