1. Update the map of data set with Build37 Shifman genetic map (B37) and save the new file as "Lyons2003_CASTxDBA_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 CAST allele from "0" to "C", DBA2 allele from "2" to "D", missing values from "=" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 

(2) Marker "D3Mit51" misses bp position in both Shifman 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); 

(3) Marker "D10Mit264" misses bp position in both Shifman map and MGI database. The primer sequences are found in MGI, but I could not find their locations from primer-BLAST in NCBI, so we could not identify the B37 bp position of this marker currently. (it is highlighted with brown color in description file); 

(4) The bp positions of marker "D6Mit46" and "D18Mit208" are missed in both Shifman 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 these markers currently (the letters are highlighted with pink color in description file); 

(5) 7 markers miss their bp positions in Shifman 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:
(1) Change the values of trait "sex" from "M" to "1" in B37 data file; 

(2) Change the name of trait "lineage" to "pgm" in B37 data file; 

(3) Could not find the the log base of trait "HDL_log" in this cross; 


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_CASTxDBA_Lyons2003.xlsx") (1st curating work is finished in 2009, files are updated on 12/13/2010).


6. Information updated on 11/9/2011: 
(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) Quality control plots (genetic map, missing genotypes plot, map comparision plot and whole genome RF plot) performed and no issues found. All quality control plots were saved in “QCReport_Lyons2003.pdf”.