1. Update the map of data set with Build37 Cox genetic map, combine the phenotype and genotype files and save the new file as "Xiong2011_129xB6_BC_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) This project used 251 SNP markers (210 rs markers and 41 customized markers) and we didn't have the Build version of the original map. The original positions of rs markers were close or very close to mouse B37 bp positions although there was a slight discrepency. It was below the level that would matter so we used the original map as B37 bp, and converted it to cM through Map Converter tool. The B37 base pair positions listed in description file was original map; 								
(2) Some markers were at the same position (cM) on chr 1,3 and 9 in B37 Cox map; 

(3) Generate genetic map plot, missing genotypes plot, map comparison plot and whole genome RF plot for B37 data and no issues were found. Since the project was a backcross and only the male mice were studied, the X chromosome was not recombinant and the genotype correlations are as expected.All quality control plots were saved in "QCReport_Xiong2011.pdf" (Information is updated on 3/23/2012); 
 

4. For the phenotypes of the cross:
No issues were found in phenotypes of this project; 

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_129xB6_BC_Xiong2011.xlsx") (1st curating work is finished on 11/23/2011).

6. Change the title of the project from "A flexible estimating equations for mapping function-valued traits in C57BL/6J and 129S1/SvImJ backcross" to "A flexible estimating equations approach for mapping function-valued traits - circadian mouse behavioral data in C57BL/6J and 129S1/SvImJ backcross" on Feb 22, 2012.

7. For any questions about the project, please contact Evan Goulding (e-goulding@fsm.northwestern.edu), or Saunak Sen (sen@biostat.ucsf.edu) (3/23/2012).