SNPtag data files were imported into Microsoft Excel and numerical values (0,1,2) were converted to A, H, B (representing AA, AB, BB). Segregation for each locus was obtained and tested for goodness-of-fit with predicted test-cross segregation (1:1) or F2-segregation (1:2:1) using chi-squared tests. Loci with significant chi-squared test statistics for goodness-of-fit for test-cross segregation (1:1) were combined with loci with significant test statistics for F2-segregation and subsequently combined into male and female data sets. These two data sets were imported as F2-formated files and separately analyzed in JoinMap 5.0 (VAN Ooijen, 2011).
Can we do that? If yes, is it possible to do it in Rqtl?
Thanks and regards
Sandip
1) I constructed a genetic map using loci with 1:1 segregation and using cross type "bc".However, I don't see any correlation with physical positions. Has anyone also experienced similar thing.
2) Is it possible to combine loci with 1:1 and 1:2:1 segregation and use for linkage map construction. I came across a paper wherein they mentioned that:SNPtag data files were imported into Microsoft Excel and numerical values (0,1,2) were converted to A, H, B (representing AA, AB, BB). Segregation for each locus was obtained and tested for goodness-of-fit with predicted test-cross segregation (1:1) or F2-segregation (1:2:1) using chi-squared tests. Loci with significant chi-squared test statistics for goodness-of-fit for test-cross segregation (1:1) were combined with loci with significant test statistics for F2-segregation and subsequently combined into male and female data sets. These two data sets were imported as F2-formated files and separately analyzed in JoinMap 5.0 (VAN Ooijen, 2011).
Can we do that? If yes, is it possible to do it in Rqtl?