1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Nishihara2007_C3HxNZO_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 missing genotypes from "U" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 


(2) The bp position of marker "D12MIT17" was missed in both Cox map and MGI. Primer sequences found in MGI, but their locations don't match the result from primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently (the letters are highlighted with pink color in description file); 


(3) Marker "D11MIT2" and "D13MIT11" missed 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 details.


4. For the phenotypes of the cross:
This project has 222 male mice in total and no problems are found in phenotypes currently;


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_C3HxNZO_Nishihara2007.xlsx") (first  curating work finished at 6/8/2009, files are updated at 7/6/2009, 10/20/2010, 1/14/2011).


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. Chr 1 had marker order problem, the last marker on chr 18 and 19 might have a map problem (observed from map comparison plot). All quality control plots were saved in "QCReport_Nishihara2007.pdf".