1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Rodriguez2009_NZWxSWR_B37_Data.csv". This file is ready to be read into Rqtl (please see genotype section for the details of map update); 


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) The original map is a mixture between 60 Mit markers and 14 author designed markers. Author provided their Mb positions based on NCBI build 36 (except marker D17MIT10 which was B33) in original data file. In B37 data file of the project, the new cM positions of MIT markers were converted from Mouse Map Converter tool in Center of Genome Dynamics web, their B37 bp positions were received from Map Converter tool, MGI website, NCBI primer-BLAST and UCSC In-Silico PCR. For the markers that couldn't find their B37 positions by these tools, their B36 positions in original file were    selected and converted into B37 bp positions through Lift Genome Annotations (http://genome.ucsc.edu/cgi-bin/hgLiftOver), then converted bp positions  to new cM by Mouse Map Converter tool. This is the same method used in author designed markers, converted their B36 bp positions to B37 through Lift Genome Annotations first, then converted bp positions to new cM by Mouse Map Converter tool. 

(2) Changed the marker names to standard format and saved the changes in B37 data file; 

(3) There were 14 author designed markers in data file. The method of marker position update has been explained above. Please see description file for more details (this type of markers is highlighted with sky blue color in description file);

(4) The bp positions of marker "D3Mit19", "D11Mit126" and 'D18Mit208" were missing in both Cox map and MGI. Primer sequences found in MGI, but their locations didn't match the result from primer-BLAST in NCBI. The original data had B36 bp positions of these markers and converted them into B37 bp positions through Lift Genome Annotations (http://genome.ucsc.edu/cgi-bin/hgLiftOver); 

(5) Marker "D17Mit10" and "DXMit16" missed 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);

(6) Markers "D4Mit18", "D4Mit28", "D10Mit10", "D11Mit2" and "D18Mit48" missed 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; 

(7) Corrected 2 genotyping errors for 2 male mice and saved the changes in B37 data -- one was on chromosome 5 (mouseid 222), the other one was on chromosome X (mouseid 257); 

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


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) Change the "pgm" from "A" (NZW strain) to 0 and save the changes in B37 data file; 


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_NZWxNZB_Rodriguez2009.xlsx") (1st curating work is finished on 7/19/2011).