1. Updated the map of data set with Build37 Cox genetic map (B37) and saved the new file as "Chesler2012_B6x129S_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) Changed the symbol of B6 allele from "B6" to "B", 129S allele from "129S" to "S", missing genotypes from "NC" (original data) to "-" (standard format in data sets of QTL archive) and saved the changes in B37 data file; 

(2) Most markers in data file were SNP markers began with "rs", the rest were the markers whose names began with "mCV", "CEL-", "UT_" and "petM-". Could not find information of 72 SNP markers in Cox genetic map and MGI database directly, got their B37 baspair positions from CGD SNP Database (http://cgd.jax.org/cgdsnpdb/) first, then converted them to cM through Mouse Map Converter tool (http://cgd.jax.org/mousemapconverter/). This type of markers was highlighted with yellow color and please see description file for details;

(3) Could not find information of 43 SNP markers in Cox genetic map and MGI database directly, got their B37 baspair positions from author and converted them to cM through Mouse Map Converter tool. This type of markers was highlighted with gold color and please see description file for details; ;

(4) Could not find information of marker "mCV24244050" in Cox genetic map and MGI database directly, blast the sequence provided by the author in UCSC Genome database to identify the B37 bp position, then converted it to cM through Mouse Map Converter tool (this type of markers was highlighted with turquoise color in description file);

(5) Could not find information of 2 SNP markers in Cox genetic map and MGI database directly, converted their B33 bp positions provided by author to B37 through UCSC coordinate conversion (http://genome.ucsc.edu/cgi-bin/hgLiftOver), then converted them to cM using Mouse Map Converter tool (this type of markers was highlighted with sea green color and please see description file for details); 

(6) Some markers were at the same position (cM) on chr 1,4,5,6,7,8,9,12,13,14,15,17 and X in B37 Cox map;
 
(7) Potential genotype errors have been detected by Rqtl program after data input -- 79 male heterozygote genotypes were found on the X chromosome; 4 SS genotypes from females from cross (BxS)x(BxS) were found on the X chromosome; 

(8) Generated genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. The markers on chr 12 had marker order problems. The quality control plots were saved as separated PNG files since the size of data was very big. 


4. For the phenotypes of the cross:
(1) Changed the empty cells from " " to "-" in trait Hypotherm and LORR BEC, saved the changes in B37 data file; 

(2) Removed extra " " from all phenotypes and saved the changes in B37 data file;

(3) One mouse (mouse ID = 358) missed all phenotype values. 


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_B6x129S_Chesler2012.xlsx") (1st curating work was finished on 3/19/2012).