1. Updated the map of data set with Build37 Cox genetic map and saved the new file as "Yi2007_M16ixCast_B37_Data.csv". 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 (Yi2007_M16ixCast_B37_Data.csv);

(2) Marker "D1MIT9" was unmapped in Cox map and its primer sequences could not be found on MGI, either. The cM position of this marker in B37 file was calculated by interpolating algorithm suggested by Gary through Rqtl, the bp position was unavailable this time (highlighted with purple color)

(3) Seven markers missed cM positions in Cox genetic map. Found their bp positions from MGI and converted them into B37 cM positions through Mouse Map converter tool. They were highlighted in yellow color and please check the 1st page of description file for details. Moreover, four of them were not standard MIT markers, they might be genes. The names of these marker were "Agouti", "GHRH", "IGF.1" and "PPAR";

(4) Marker "D2MIT174", "D13MIT263", "D14MIT42" and "D19MIT6" 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. Please check the 1st page of description file for the details (these markers are highlighted with green color). Among them, the primer size of marker "D2MIT174" in MGI was different from NCBI. In MGI, it was 148; in NCBI, the size of the closest BLAST result was 456; 

(5) Six markers missed bp positions in Cox map, their positions were assigned from MGI database (this type of markers are highlighted with orange color in description file);
 
(6) Marker "D6NDSS" was unmapped in Cox map. Its primer sequences found in MGI, and its bp position was identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (this type of markers is highlighted with grey color in description file)

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


4. For the phenotypes of the cross:
(1) Changed the name of trait "ID" into "id" in B37 cross file so the data file should not be treated as SYLK file by EXCEL;

(2) Couldn't find the definitions of trait "scfat12wk" and "gfat12wk" in papers and I labelled them as "not in paper" in description file;

(3) Unlike the projects I curated before, the authors used "1" represent male mouse and "2" represent female mouse in sex for this cross file

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_M16ixCast_Yi2007.xlsx"). (first curating work finished at 3/13/2010, files are updated on 11/23/2010).


6. Information were updated on 5/30/2012:
Change the name of the map (from "Shifman" to "Cox" map) in description and readme file, add a map reference in description file.