Windows QTL Cartographer 2.5 - FTP Directory Listing

More documents

Recommendations

Info

60 Windows QTL Cartographer 2.5 Create a QTL mapping result file (*.QRT) and open it in the Graph window Create a QTL summary information file using the EQTL function. Display a confirmation box asking if you want to display QTL summary information in the Main window's Data pane. Composite Interval Mapping What it is Composite interval mapping (CIM) adds background loci to simple interval mapping 58 (IM). CIM fits parameters for a target QTL in one interval while simultaneously fitting partial regression coefficients for "background markers" to account for variance caused by non-target QTL. "In theory, CIM gives more power and precision than simple IM because the effects of other QTL are not present as residual variance. Furthermore, CIM can remove the bias that would normally be caused by QTL that are linked to the position being tested." Background markers are usually 20-40cM apart. High-level workflow Here's a quick overview of how to use WinQTLCart's CIM implementation. The first few times you run this analysis, go with the WinQTLCart default values for the form's parameters. The defaults provide the best all-around parameter settings, especially for initial analysis sessions. 1. Select the CIM analysis method. 2. Select the chromosome(s) and trait(s) you want to analyze. 3. Select a threshold level to apply to the selected trait(s). Select either By manual input 57 (the WinQTLCart default) or By permutations 57 (to have WinQTLCart determine an optimum threshold). See the Setting the threshold level 56 topic for more information on the impact of each of these choices. 4. Click OK to start the calculations for the threshold level. This may take from several minutes to several hours to run. 5. Following threshold calculation, set CIM form parameters 60 . Select a walk speed in cM. It's recommended you use the same walk speed for your entire dataset. Don't reset the walk speed between runs or your results will not be comparable. 6. Click Start to begin the analysis. The analysis may take from 20 minutes to several hours to run. Running composite interval mapping analysis WinQTLCart provides default values for the parameters in this form. The defaults provide the best allaround parameter settings, especially for initial analysis sessions. Composite interval mapping analysis uses WinQTLCart source data mapping files (.MCD files). Use WinQTLCart's import commands to move your source data files from text to .MCD format. 1. Open a source data file into the WinQTLCart main window. 2. Select Method>Composite Interval Mapping. WinQTLCart displays the CIM analysis controls in the form pane. © 2010 N.C. State University, Bioinformatics Research Center
3. Click Result File… to select the .QRT file you want to create. 4. Click the Control… button to display the Set CIM Control Parameters dialog. © 2010 N.C. State University, Bioinformatics Research Center WinQTLCart Procedures 61 4a. For the CIM Model field, specify the markers to be used as cofactors in the CIM analysis: Model 1: All Marker Control—Use all the markers to control for the genetic background. Model 2: Unlinked Marker Control—Use all unlinked markers to control for the genetic background. Model 6: Standard Model—The default model that selects certain markers as control markers by using additional parameters: control marker number and window size. Selecting this model requires you to fill in extra fields on the dialog: Control marker numbers, Window size (cM), and Regression method selection (all explained below). 4b. Click Set control markers manually if you do not want WinQTLCart to automatically select the control markers. This will display a dialog box after you start the analysis so that you can
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 27 and 28: © 2010 N.C. State University, Bioi
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 and 38: 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 63: © 2010 N.C. State University, Bioi
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 91 and 92: Credits & acknowledgements © 2010
Page 93: QTL Cartographer 1, 4 export format
show all

Windows QTL Cartographer 2.5 - FTP Directory Listing

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?