1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Sugiyama2002_BALBxCBA_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 CBA allele from "0" to "C", BALB allele from "2" to "B", heterozygous allele from "1" to "H", missing genotypes from "=" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 

(2) Could not find bp position of marker "D12MIT145" in Cox genetic map or MGI databases. No primer sequences are available from MGI, either. We could not identify the B37 bp position for this marker currently (marker is highlighted with pale blue color in description file);

(3) Marker "D4Mit26" misses bp position in both Cox map and MGI database. Primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (it is highlighted with green color in description file); 

(4) The bp positions of marker "D3MIT19" and "D4MIT234" are 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 positions of them currently (the markers are highlighted with pink color in description file); 

(5) Unable to find cM position of marker "D12Nds2" from Cox map directly, bp positions assigned based on MGI, then convert it to cM through Map Converter tool (this type of marker is highlighted with light yellow color in description file); 

(6) Five markers miss 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.

(7) Potential genotype errors have been detected by Rqtl program after data input -- 7 male heterozygote genotypes are found on the X chromosome; 


4. For the phenotypes of the cross:
This project only had F2 male mice (n=208) from BALBxCBA intercross, no more problems are detected in phenotypes;


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_BALBxCBA_Sugiyama2002.xlsx") (1st curating work is finished in 2009, files are updated on 2/10/2011).


6. Information were updated on 5/25/2012:
Change the name of the map (from "Shifman" to "Cox" map) in description and readme file, add a map reference in description file.