1. The original cross file had 1407 SNP markers, the basepair positions of them were based on Build36. Most of their marker names were in standard format and could be converted into Build 37 positions through our Mouse Map Converter tool. Only 187 markers didn't have standard names and they were converted through UCSC Lift Genome Annotations database, please see the details in (3); 


2. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Jarvis2011_SMxLG_B37_Data.csv". This file is ready to be read into Rqtl; 


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


4. For the genotypes of this cross: (cM=centimorgan, bp=basepair)
(1) This project used 1407 SNP markers, among them, 187 markers missed new positions in both Cox map and MGI database. They had basepair positions of B36 in original file, converted them into B37 basepair positions through 
UCSC Lift Genome Annotations database, then converted them into B37 cM positions through our Mouse Map Converter tool (these markers were highlighted with tan color and please see description file for details);

(2) The cross file only had 19 autosomes;

(3) Some markers are at the same position (cM) on chr 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18 in B37 Cox map; 


5. For the phenotypes of the cross:
(1) The cross type of the experiment was F10 generation of an advanced line between SM and LG strain, but the information of F1 cross direction is not found in paper (highlight in blue color);

(2) Change the symbol of female mouse in "sex" trait from "F" to "0", male mouse from "M" to "1", saved the changes in B37 data file;


6. Except the "csv" file 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_SMxLG_Jarvis2011.xlsx") (1st curating work is finished in 3/17/2011).


7. Information updated on 10/27/2011: 
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 every chromosome in this cross (each chromosome had markers correlate to other chromosomes). All the genotype diagnostic plots were saved as PNG files since the project had more than 1000 mice and markers. The size of the pdf file is too big to open.