1. The project includes 2 cross files -- DBA/2xNMRI8 and DBA/2xDU6i cross. Update the map of datasets with Build37 Cox genetic map and save the new files as "Brockmann2009_DBA2xNMRI8_B37_Data.csv" and "Brockmann2009_DBA2xDU6i_B37_Data.csv" in folder "Brockmann_2009a" and "Brockmann_2009b". These files are ready to be read into Rqtl. This is the readme file of cross DBA/2 x NMRI8;  


2. Generate a description file of the project, it includes the general information, definitions of phenotypes, description of genotypes and information of missing markers;


3. For DBA2 x NMRI8 cross, there are 275 mice (142 Female + 133 Male), 98 markers, 18 phenotypes in total;


4. For the genotypes of NMRI8 x DBA2 cross: (cM=centimorgan, bp=basepair)
(1) Find potential typo errors in 14 marker names. Change them in map updating file (B37). The names of markers before and after correction have been listed in the description file, they are highlighted by blue color;
original file	NMRI8xDBA2_B37_Data_Brockmann.csv"
D1Mit16a   --> 	D1Mit16
D2Mit6a	   -->	D2Mit6
D5Mit24a   -->	D5Mit24
D5Mit221a  -->	D5Mit221
D6Mit138a  -->	D6Mit138
D7Mit250a  -->	D7Mit250
D7Mit253a  -->	D7Mit253
D7Mit259a  -->	D7Mit259
D12Mit141a -->	D12Mit141
14Mit257   -->	D14Mit257
D15Mit193a -->	D15Mit193
Dx9Mit192  -->	DXMit192
DX9Mit119  -->	DXMit119
DX9Mit95   -->	DXMit95a

(2) Marker "DMit266" missed both cM and bp positions in Cox genetic map, got the bp information of the marker from MGI database, then converted it into cM through Map Converter tool (This marker was highlighted by yellow color in description file);

(3) Three markers missed bp positions in Cox map, found their bp information from MGI database. These markers were highlighted with orange color and please check the 1st page of description file for the details;

(4) Marker "D4Mit205" and "D7Mit26" missed bp positions in both Cox map and MGI database. Their primer sequences were found in MGI, and their bp locations were identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (these markers were highlighted with green color and please check the description file for the details);


5. For the phenotypes of the cross DBA2 x NMRI8:
(1) The definitions of the traits were described in Brockmann's previous paper (reference 3)
QTLs for pre- and postweaning body weight and body composition in selected mice. Mamm Genome 15: 1-15, 2004
not in current paper

(2) Could not find the definition of "pedigree" from both publications;


6. Except the "csv" file mentioned above, I also saved the description file, original data, data with B37 map, working record and list of missing markers together as a big excel file ("Data_Description_DBA2xNMRI8_Brockmann2009.xlsx")  (the 1st curation work is finished on 11/20/2009, file is updated at 8/4, 10/13, 10/26/2010)


7. Information updated on 10/5/2011: 
(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) Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. Markers on chr 4 had marker order problems. All quality control plots were saved in "QCReport_Brockmann2009a.pdf".