Windows QTL Cartographer 2.5 - FTP Directory Listing

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34 Windows QTL Cartographer 2.5 Working with a source file's basic information At the Source data manipulations pane on the Main window, click the Basic Info button to open the Manipulation of Basic Information dialog. Symbol for missing trait value. Enter a symbol to use for missing traits value, based on your trait data. Marker translation table. Edit or add symbols you want to use for these genotype markers; you can enter any alphanumeric character(s) as a symbol. These translations apply to the experimental design you selected at the left of the dialog. Note WinQTLCart assumes that the A allele is diagnostic for the High (parental 1) line and the a allele is diagnostic for the Low (parental 2) line. A minus sign (-) means the allele is unknown. WinQTLCart uses the numbers (2, 1, 0, 12, 10, -1) to determine how to encode the output of the genotypes. The alphanumeric tokens you enter here indicate how you have coded the markers in the source data. Cross Information Select the experimental design option based on your data. You can select only one option. B1. Backcross, with 1=parental line to which the F1 line was crossed. B2. Backcross, with 2=parental line to which the F1 line was crossed. Ri0. Recombinant inbred line, derived by doubled haploid lines. Ri1. Recombinant inbred line, derived by selfing. Ri2. Recombinant inbred line, derived by sib mating. SF. Selfed intercross line. Enter an integer indicating the generation. Limit of 2. RF. Randomly mated intercross line. Enter an integer indicating the generation. © 2010 N.C. State University, Bioinformatics Research Center
© 2010 N.C. State University, Bioinformatics Research Center WinQTLCart Procedures 35 T(B1)SF. Test cross, with genotyping done on an intercross (SF) and phenotyping on a cross (B1) derived from that intercross. Enter an integer indicating the generation. T(B1)RF. Test cross, with genotyping done on an intercross (RF) and phenotyping on a cross (B1) derived from that intercross. Enter an integer indicating the generation. T(B2)SF. Test cross, with genotyping done on an intercross (SF) and phenotyping on a cross (B2) derived from that intercross. Enter an integer indicating the generation. T(B2)RF. Test cross, with genotyping done on an intercross (RF) and phenotyping on a cross (B2) derived from that intercross. Enter an integer indicating the generation. Map Function A map function is a mathematical relationship between recombination probabilities and map distances. Select the function you want, based on the interference to be assumed. Haldane. The default option. Assumes no crossover interference. Kosambi. Assumes some interference. Fixed. The Morgan mapping function. Assumes complete interference. Note These mapping functions, among others, are discussed at length in Ben Lui's book, Statistical Genomics: Linkage, Mapping and QTL Analysis (1998). Distance type Position. Indicates that the numbers indicate positions from the left telomere of the current chromosome. This means the numbers should be in increasing order. Interval. Indicates that the numbers are for the interval distance after a marker. This means that the last number, and the last number only, should be zero. Distance units centiMorgan (cM). Very small. 100 centiMorgans=1 Morgan. Morgan. The distance over which, on average, one crossover occurs per meiosis. Recombination. Percentage of crossover events that occur between two markers. Related Topics MCD file format 39 Working with source file's individual information At the Source data manipulations pane on the Main window, click the Individual button to open the Add or Delete Individuals dialog.
Page 1 and 2: Windows QTL Cartographer 2.5 User M
Page 3 and 4: Contents WinQTLCart Procedures 25 S
Page 5 and 6: About Windows QTL Cartographer WinQ
Page 7 and 8: These are all text files that you c
Page 9 and 10: © 2010 N.C. State University, Bioi
Page 11 and 12: Main window - Menus - Help Icon Com
Page 13 and 14: Main window tour © 2010 N.C. State
Page 15 and 16: Tree Item Action Function © 2010 N
Page 17 and 18: Graph window - Menus - File Command
Page 19 and 20: Graph window - Menus - Tools Comman
Page 21 and 22: Row Number> Increase graph number i
Page 23 and 24: Related topics Graph Window - Menus
Page 25 and 26: Selecting chromosomes for graph dis
Page 29 and 30: Related topics Creating simulation
Page 33 and 34: Note: © 2010 N.C. State University
Page 35 and 36: C. MCD file (only selected traits a
Page 37: Changing a cell's contents © 2010
Page 41 and 42: Working with source file's chromoso
Page 43 and 44: Working with source file's other tr
Page 49 and 50: Fill in the dialog based on your so
Page 53 and 54: First to specify raw data file's nu
Page 65 and 66: 3. Click Result File… to select t
Page 67 and 68: 6. Select one or all chromosomes to
Page 69 and 70: Epistasis. Number of epistatic gene
Page 77 and 78: file with Windows notepad. © 2010
Page 85 and 86: Tutorials A chromosome graphic befo
Page 87 and 88: Create new source data file © 2010
Page 89 and 90:
© 2010 N.C. State University, Bioi
Page 91 and 92:
Credits & acknowledgements © 2010
Page 93:
QTL Cartographer 1, 4 export format
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