1. This project (Burke_2012) included 2 data sets of a 4-way cross between inbred strain BALB/cJ, C57BL/6J, C3H/HeJ and DBA/2J. The direction of the cross was (BALBxB6) F1 x (C3HxDBA/2) F1. The 1st one had 505 female mice, the 2nd one was merged from the initial population and a replicate population (n=832). They were saved in 2 separated folders (ÒBurke_2012aÓ and ÒBurke_2012bÓ). This is the data set of ÒBurke_2012bÓ. The map of the data was updated with Build37 Cox genetic map (B37) and the new file was saved as "Burke2012b_4way_B37_Data.csv". This file was ready to be read into Rqtl.


2. Generated a description file of the project, it included 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) The original data of ÒBurke_2012aÓ didn't have detailed information of genetic map. It was merged from the data set of "Burke_2012a" and the data of replicate population by the author. Unlike "Burke_2012a", it only had SNP markers and each marker was used in one side of parental strains. All the genotypes in B37 data have been converted to the codes which can be read by Rqtl. The coding of genotypes were listed as following:
In original file: 1=BALB/cJ, 2=C57BL/6J, 3=C3H/HeJ, 4=DBA/2J, 0=genotype could not be scored
In B37 data file: 1=BALB|C3H, 2=B6|C3H, 3=BALB|DBA, 4=B6|DBA, 5=BALB, 6=B6, 7=C3H, 8=DBA, "-"=missing 
The markers with converted genotypes have been rearranged in B37 data by the chromosome ID and basepair positions; 

(2) Could not find any information of marker "rs3089783" and "rs3023673" in Cox genetic map and MGI database directly, got their B37 basepair positions from CGD SNP Database (http://cgd.jax.org/cgdsnpdb/) first, then converted them to cM through Mouse Map Converter tool (this type of markers was highlighted with light yellow color in description file);

(3) Some markers were at the same position (cM) on chr 14 in B37 Cox map in this data;
 
(4) Generated genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. Chr 4 and 6 had correlated markers in RF plot. All quality control plots were saved in "QCReport_Burke2012b.pdf". 


4. For the phenotypes of the cross:
(1) Changed the symbol of missing values from "" to "-" and saved the changes in B37 data file; 

(2) Added sex information (0 = female; 1=male) in B37 data file; 


5. Except the "csv" and "pdf" files 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_4way_Burke2012b.xlsx") (The 1st curating work was finished on 5/2/2012).