1. Updated the map of data set with Build37 Cox genetic map, the new file was saved as "Beamer1999_B6xCAST_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) Change the symbol of B6 allele from "A" -> "B", CAST allele from "B" -> "C", missing genotypes from "=" to "-" in B37 data file; 

(2) 9 markers didn't have bp positions in Cox map, assigned their bp positions from current MGI database (this type of markers was highlighted by gold color in description file);

(3) Marker "D3Mit120" missed bp position in both Cox map and MGI. Its Primer sequences were found in MGI, but their locations didn't match the result from primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently and it was highlighted with rose color in description file;

(4) Marker "D14Mit160" missed bp position in both Cox map and MGI. Its Primer sequences were found in MGI, but the fragment product size did't match the result from primer-BLAST in NCBI. We could not identify the B37 bp position of this marker and it was also highlighted with rose color in description file;

(5) Marker "D10Mit151" missed bp positions in both Cox genetic map and MGI, its 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 lime color in description file); 

For the details, please see the annotation of these markers in description file.


4. For the phenotypes of the cross:
The trait "PC1" and "PC2" were not defined, they could be principal component


5. Except the "csv" file mentioned above, saved the description file with original data, data with B37 map and missing marker list together as a big excel file ("Data_Description_B6xCAST_Beamer1999.xlsx"). (first curating work finished at 6/4/2008, files were updated in 8/10/2010, 10/6, 10/25, 11/17/2010, 8/30, 9/1/2011).


6. Information were updated on 9/29/2011):
(1) Change the name of the map (from "Shifman" to "Cox" map) in description and readme file; 

(2) Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. Problematic markers were found on chr 8 (correlated with chr 6) and chr 13 (marker order). All quality control plots were saved in "QCReport_Beamer1999.pdf".