1. Updated the map of the data set with Build37 Cox genetic map (B37) and savedd the new file as "Dzur-Gejdosova2012_PWDxB6_BC_B37_Data.csv". This file was ready to be read into Rqtl.


2. Generated a description file of the project, it included 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) Changed the symbol of missing genotypes from " " (original data) to "-" (standard format in data sets of QTL archive) and saved the changes in B37 data file; 

(2) Unable to Found any informatoin of marker "D17Zt634" and "DXSr62" in Cox map. The author of the project provided B37 bp positions of these two markers, then they were converted into cM through Map Converter tool (this type of markers was highlighted with tan color in description file);

(3) Marker "D2Mit266" was unmapped in Cox genetic map. The bp position of the marker was assigned based on MGI, then converted it into cM through Map Converter tool (this type of markers was highlighted with light yellow color in description file); 

(4) Marker "D14Mit228" and "D16Mit55" 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 was highlighted with lime color in description file);

(5) The bp position of marker "D14Mit75" was missing in both Cox map and MGI. No primer sequences were available for it in MGI. We could not identify the B37 bp position of this marker currently (this type of markers was highlighted with pale blue color in description file);

(6) Six markers missed bp positions in both Cox map and MGI. Primer sequences 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 those markers currently. This type of markers was highlighted with rose color in description file and please see description file for details;

(7) Six markers missed bp positions in Cox genetic map, assigned the positions from current MGI database. This type of markers were highlighted with gold color and please see description file for details; 

(8) Generated genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. Chr 3 and chr 4 had correlated markers. The markers on chr 10 and chr 14 might have marker order problems. All quality control plots were saved in "QCReport_Dzur-Gejdosova2012.pdf". 


4. For the phenotypes of the cross:
Changed the name of trait "ID" to "mouseID", added the sex information of mice and saved the changes in B37 data file. 


5. Except the "csv" and "pdf" files 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_PWDxB6_BC_Dzur-Gejdosova2012.xlsx") (1st curating work was finished on 2/27/2012).