1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Mathews2003_ALRxNOD_BC_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 NOD allele from "0" to "D", heterozygous allele from "1" to "H" (standard format in data sets of QTL archive) and save the changes in B37 data file; 

(2) This project only has female mice so the genetic map of B37 data file is female Centimorgans, the positions on X chromosome are sex-averaged Centimorgans;

(3) Change the marker names into the standard DMit markers from The Jackson Laboratory Mouse Genome Informatics Database, save the changes in B37 data file;

(4) Marker "D1Mit8", "D2Mit238" and "D4Mit18" miss bp positions in Cox genetic map, assign the positions from current MGI database (this type of markers is highlighted with gold color in description file);

(5) The bp position of marker "D2Mit190" is missing in both Cox map and MGI. Primer sequences found in MGI, but no target templates were found in primer-BLAST in NCBI. We could not identify the B37 bp positions of these markers currently (this type of markers is highlighted with dark yellow color in description file);

(6) Marker "D3Nds6" is unmapped in Cox genetic map. The bp positions assigned based on MGI, then convert it into cM through Map Converter tool (http://cgd.jax.org/mousemapconverter/) (this type of markers is highlighted with light yellow color in description file and please see description file for details); 

(7) Marker "D11Mit126" and "D14Mit160" miss bp positions in both Cox map and MGI. Primer sequences found in MGI, but their locations or the fragment product size 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); 

(8) Could not find any information of marker "D15Mit51.2" 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); 

(9) Marker "D17Nds3" is unmapped in Cox map. To get bp position, primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR. Next, convert the bp into cM through Map Converter tool (this type of markers is highlighted with tan color and please see description file for details); 


4. For the phenotypes of the cross:
(1) The information of intervention (type of diet) is not found in paper (highlight in blue color);

(2) The original data didn't have information of mouse sex, find it in paper (all the mice were female) and add column of sex in B37 data file; 


5. Except the "csv" file mentioned above, I also save the description file, original data, data with B37 map, data process and list of missing markers together as a big excel file ("Data_Description_ALRxNOD_BC_Mathews2003.xlsx") (1st curating work is finished on 7/29/2011).


6. Information updated on 11/17/2011: 
(1) Change the Build37 Cox genetic map from Female Centimorgans to Sex-Average Centimorgans (suggested by Gary), save the changes in B37 data file and 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. Problematic markers were found on chr 2, 4, 11 and 17 (chr 17 had marker order problem). All quality control plots were saved in "QCReport_Mathews2003.pdf".