1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Shimomura2001_BALBxB6_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) Marker "D3Mit19", "D8Mit14" and "D12Mit260" miss bp positions 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 (this type of markers is highlighted with rose color in description file and please see description file for details);

(2) Marker "D10NDs1" is unmapped in Cox map. Primer sequences found in MGI, but their locations don't match the result from NCBI primer-BLAST. The interpolating algorithm doesn't work for the marker in this cross, so we set the position of the marker as 1 cM for this data file, the bp information is unavailable (this type of markers is highlighted with light gray color in description file and please see description file for details);

(3) Marker "D10Mit51", "D14Mit228" and "D17Mit18" miss 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 and please see description file for details);

(4) Nine markers miss 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); 

(5) Marker "D10Mit264" miss bp position in both Cox map and MGI. Primer sequences found in MGI, but their locations could not be found from primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently (this type of markers are highlighted with dark yellow color and please see description file for details); 

(6) Marker "D19Mit93" is unmapped in Cox genetic map, the primer sequences could not be found in MGI, either. The interpolating algorithm doesn't work for the marker in this cross, so we set the position of the marker as 1 cM for this data, the bp information is unavailable (this type of markers is highlighted with lavender color in description file);

(7) The 14th marker on chromosome 12 didn't have a standard marker name, it was called "vip" in original data file. We could not find any information of this marker in Cox genetic map or current databases. Use interpolating algorithm in Rqtl to calculate the B37 cM position, the bp information is unavailable (this type of markers is highlighted with bright green color in description file);

(8) Some markers are at the same position (cM) in B37 Cox map; 

(9) The original data didn't have "pgm" information. The cross only had one cross direction (BALBxB6)x(BALBxB6). Add "pgm" (pgm=0) column in B37 data so the program can detect the genotype errors automatically; 

(10) Potential genotype errors have been detected by Rqtl program after data input -- 9 male heterozygote genotypes are found on the X chromosome, 8 female BB genotypes are found on X chromosome from cross (CxB)x(CxB); 


4. For the phenotypes of the cross:
(1) The information of intervention (type of diet) and mouse age at testing are not found in paper (highlight in blue color);

(2) The definition of trait "chitau", "ontau", "tauoff", "alpha", "sdon", "offsd" and "onoff" are not found in paper; 

(3) The original data file used 1 representing female and 0 representing male mouse in sex column, I reversed them in B37 data file according to the Rqtl program requirement; 

(4) Add column of "pgm" in B37 data file (see [9] in genotypes section above); 


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_BALBxB6_Shimomura2001.xlsx") (1st curating work is finished on 8/18/2011).