1. Updated the map of data set with Build37 Cox genetic map and saved the new file as "Ankra-Badu2009_M16ixL6_B37_Data.csv". The map in original file was Mb/2, the new map in B37 file was new cM. The file is ready to be read into Rqtl;


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


3. For the genotypes of the cross (cM=centiMorgan, bp=basepair)
(1) Dropped all artificial "begin" and "end" markers from the original data set, saved the changes in map updating file (Ankra-Badu2009_M16ixL6_B37_Data.csv);

(2) Marker "D12NDS11" was unmapped in Cox map and its position from MGI was conflict to the marker in cross file. The interpolating algorithm didn't work for this marker, so it was dropped from B37 data file (suggested by Gary in 3/18/2010)

(3) Marker "D10NDS1" was unmapped in Cox map and its primer sequences do not match the result from primer-BLAST in NCBI. The interpolating algorithm didn't work for this marker and it was dropped from B37 data file, too. (suggested by Gary in 3/18/2010) (These two dropped markers were highlighted with red color in description file)

(4) Eight markers missed bp positions in Cox genetic map. Assigned their bp positions from current MGI database (this type of markers were highlighted with orange color in description file);

(5) Marker "D15MIT1" didn't have new cM position in Cox map. Found its bp positions from MGI and converted Mb into B37 cM position through Mouse Map converter tool. It was highlighted in yellow color and please check the description file for details;

(6) Marker "D16MIT55" and "D17MIT10" missed bp positions in both Cox genetic map and MGI, their primer sequences were found in MGI, and their bp locations were identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (this type of markers was highlighted with grey color in description file)

(7) There was no X chromosome in this data file


4. For the phenotypes of the cross:
The authors used "1" represent male mouse and "2" represent female mouse in sex for this cross file. Changed "2" to "0" in trait "sex" in B37 data file so it has same format as other projects in QTL archive. 


5. Except the "csv" file mentioned above, save the description file, original data, data with B37 map, data process record and missing marker list together as a big excel file ("Data_Description_M16ixL6_Ankra-Badu2009.xlsx"). (first curating work finished on 3/19/2010, files were updated on 10/26/2010)


6. 9/28/2011: 
(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 "QCReport_Ankra-Badu2009.pdfÓ.