1. Update the map of data set with Build37 Shifman genetic map (B37) and save the new file as "DiPetrillo2004_C3HxSWR_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 missing genotypes from "U" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 

(2) Could not find any information of marker "D9Mit8-46" in Shifman genetic map or current databases. Use interpolating algorithm in Rqtl to calculate the B37 cM position of it, the bp position is unavailable (marker is highlighted with aqua color in description file);

(3) Marker "D6Mit198" is unmapped in Shifman genetic map, the primer sequences could not be found in MGI, either. Use interpolating algorithm in Rqtl to calculate the B37 cM position, the bp information is unavailable (this marker is highlighted with purple color in description file);

(4) Marker "D4Mit26" 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); 

(6) Marker "D13Mit256" misses bp position in both Shifman map and MGI database. No primer sequences are available from MGI. We could not identify the B37 bp position for this marker currently (it is highlighted with blue color in description file); 

(7) The bp position of marker "D18Mit208" is 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 this marker currently (the letters are highlighted with pink color in description file); 

(8) 5 markers miss their bp positions in Shifman genetic map, assign the position 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) The information of intervention (type of diet) is not found in paper (highlight in blue color);

(2) Remove redundant trait "Pedigree" (it equals to trait "mouse") from B37 data file; 

(3) This is a reciprocal intercross but the data file doesn't have the information of paternal grandma (pgm, which indicates the direction of cross), Rqtl generates a column named "pgm" automatically after the data input;

(4) Find a value "94a" in trait "mouse" in data file (B37 data). It is interpreted as missing value in Rqtl after data input.


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_C3HxSWR_DiPetrillo2004.xlsx") (1st curating work is finished on 10/30/009, files are updated on 10/20/2010)


6. Information updated on 10/12/2011: 
(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 ÒQCReport_DiPetrillo2004.pdfÓ.