1. This project included 2 data sets --- data set of P-selectin v2 (P-selectin v2.csv) and Vcam1 (Vcam1.csv). The only difference between them was the phenotypes. They were merged into one data set and the new file was saved as "Yuan2008_B6xC3H_B37_Data.csv" with Build37 Cox genetic map. 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) Correct typos in marker names (change "DM" to "DMit") and save the changes in B37 data file; 

(2) Marker "D3Mit19" and "D14Mit185" missed bp positions in both Cox map and MGI. Primer sequences found in MGI, but their locations don't match the results from primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently (this type of markers is highlighted with rose color in description file);

(3) Marker "D7Mit71" and "D18Mit34" missed bp positions in both Cox map and MGI. Primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (this type of markers is highlighted with lime color in description file);

(4) We found a conflict of marker "D13Mit63" position between map converter tool and MGI. After checked the diagnostic plots of the cross, we decided to use the bp position from MGI, then convert it to cM through our tool (this marker is highlighted with light yellow color in description file);

(5) 11 markers missed bp positions in Cox genetic map, assign the positions from current MGI database. This type of markers are highlighted with gold color and please see description file for details; 

(6) Potential genotype errors have been detected by Rqtl program after data input -- 14 homozygous C3H genotypes are found on X chromosome of females in (B6xC3H)x(B6xC3H);

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


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_B6xC3H_Yuan2008.xlsx") (1st curating work is finished on 8/26/2009, files are updated on 3/3, 3/8/2011).


6. Information were updated on 5/30/2012:
Change the name of the map (from "Shifman" to "Cox" map) in description and readme file, add a map reference in description file.