QTX. Tutorial for. by Kim M.Chmielewicz Kenneth F. Manly. Software for genetic mapping of Mendelian markers and quantitative trait loci.

Transcription

1 Tutorial for QTX by Kim M.Chmielewicz Kenneth F. Manly Software for genetic mapping of Mendelian markers and quantitative trait loci. Available in versions for Mac OS and Microsoft Windows. revised for QTXb17 software by Jane M. Meer, Kenneth F. Manly, Robert H. Cudmore, Jr. Roswell Park Cancer Institute October, 2002

2 Development and distribution of the Map Manager programs have been supported by subcontracts from NIH grant HG00330 from The Jackson Laboratory, by a grant from The Rockefeller Foundation, and by grant HG01656 from the National Human Genome Research Institute. This manual copyright 2002, Kenneth F. Manly

3 Table of Contents Table of Contents Page i Table of Contents... i List of Figures...1 Basic QTX functions...1 Introduction and definitions Datasets... 1 Trait values... 1 Progeny... 2 Genotypes... 2 Selecting a dataset Opening a dataset window...3 Opening a dataset file...3 Creating a new dataset...3 Opening, closing, and saving current datasets Creating a new dataset Entering marker genotype data Correcting marker genotypes Entering trait phenotype data Adding progeny to datasets Adding new progeny to a current dataset...15 Copying progeny between datasets...15 Creating a custom progeny order Importing files Importing genotypes from a spreadsheet file...22 Importing trait values from a spreadsheet file...25 Importing genotypes from a word processing file...26 Importing trait values from a word processing document...29 Importing genotypes from a Jackson Laboratory file...30 Importing genotypes from a Mapmaker/QTL file...34 Importing map distances...36 Exporting files Exporting genotypes...38 Exporting trait values...39 Exporting genotypes for selected chromosomes/loci...40 Exporting genotypes for selected progeny...41 Exporting Mapmaker/QTL files...42 Exporting Cartographer files...44 Exporting map distances...45 Exporting into QGene...47 Exporting into Pseudomarker...48 Exporting report window contents...49 Index...53

4 Page ii Table of Contents

5 List of Figures Page 1 List of Figures Figure 1. A QTX dataset window showing the number of chromosomes, number of loci per chromosome, and number of progeny Figure 2. The Stat (statistics) view of chromosome 1 from the previous dataset Figure 3. The Geno (genotype) view of chromosome 1 from the previous dataset Figure 4. The Set menu in QTX listing datasets with active and inactive windows Figure 5. The QTX window menu with the Close command highlighted Figure 6. A dataset window header Figure 7. The Set Edit dialog box Figure 8. A new dataset window after setup Figure 9. A new chromosome dialog box Figure 10. A new locus dialog box Figure 11. A new locus dialog Figure 12. A new trait dialog Figure 13. A new progeny dialog Figure 14. The dataset windows for Import 1, the destination dataset, and Import 2, the source dataset Figure 15. The genotype window for chromosome 1 in the source dataset, Import Figure 16. Progeny number 3 in the source dataset is currently selected Figure 17. The range of progeny numbers 3-7 is selected Figure 18. The progeny orders dialog on the left shows the internal progeny order about to be copied, and the dialog on the right shows the internal progeny order after being copied Figure 19. The default new progeny order name is highlighted for overtyping Figure 20. A chromosome showing the new order activated in the Progeny Orders window after being added to the dataset Figure 21. Progeny member 1 in this dataset is selected to be moved Figure 22. Progeny member 1 in this dataset has been moved Figure 23. A spreadsheet file formatted correctly for import that contains loci names and genotypes Figure 24. A spreadsheet file formatted correctly for import that contains loci names and genotypes, plus chromosome and progeny names Figure 25. The correct import settings for the Import 1 file, containing loci names and genotypes Figure 26. The correct import settings for the Import 2 file, containing chromosome, loci, and progeny names plus genotypes Figure 27. The dataset windows for the Import 1 and Import 2 files Figure 28. A spreadsheet file correctly formatted for import containing trait names and values Figure 29. The trait window following the successful import of a trait value file Figure 30. Import 8, a correctly formatted word processing file for import containing loci names and genotypes Figure 31. Import 6, a correctly formatted word processing file for import containing progeny and loci names in addition to genotypes

6 Page 2 List of Figures Figure 32. The correct import settings for Import 6, the file containing progeny and loci names in addition to genotypes Figure 33. The dataset windows for the Import 8 and Import 6 files Figure 34. Import 6, a correctly formatted word processing file for import containing trait names and values Figure 35. The trait window following the successful import of trait values from the Import 6 file Figure 36. The Jackson Laboratory webpage from which you can download RI data.. 31 Figure 37. The Jackson Laboratory webpage from which you can download backcross and intercross data Figure 38. A downloaded Jackson Laboratory file opened in a word processing application Figure 39. The correct import settings for a Jackson Laboratory file, as it contains references in addition to chromosome names, plus genotypes Figure 40. The dataset window of an imported Mapmaker file Figure 41. The dataset window of an imported Mapmaker file before linkage groups are set is on the left, and the dataset window after linkage groups are set is on the right Figure 42. The Group 1 chromosome window of a Mapmaker file before linkage groups are set; loci are unlinked because they are not in the correct order Figure 43. The Group 1 chromosome window of a Mapmaker file after linkage groups are set; loci numbers are linked because they are in a good order Figure 44. A correctly formatted word processing file with map distances between loci for import Figure 45. Changing from genotype view to map view in the Import 1 file to view map distances Figure 46. The Import 1 map distances as seen in map view Figure 47. The default export text settings Figure 48. The dataset window for the exported Import 1 genotype file is shown above, and the exported genotype file itself is shown below as text Figure 49. An exported trait value file viewed in text format Figure 50. The default export file settings for a genotype file Figure 51. A selected progeny individual in the chromosome window Figure 52. The control dialog for exporting Mapmaker files Figure 53. The file save dialog showing the default filename for a Cartographer export map file Figure 54. The file save dialog showing the default filename for a Cartographer export genotype file Figure 55. The alert that appears if a chromosome is selected; in this case, Chr Figure 56. The alert that appears if no individual chromosomes are selected Figure 57. The file save dialog showing the default filename for an export map file Figure 58. An exported map distances file displayed in text format Figure 59. The file save dialog displaying the default filename for an export QGene map file Figure 60. The file save dialog displaying the default filename for an export QGene genotype file Figure 61. A QGene export map file in text format

7 List of Figures Page 3 Figure 62. A QGene exported genotype file in text format Figure 63. The file save dialog displaying the default filename for an export Pseudomarker file Figure 64. An exported Pseudomarker file displayed in text view Figure 65. A marker regression report window Figure 66. The file save dialog displaying the default filename for an exported marker regression report Figure 67. The file save dialog displaying the default filename for an exported interval mapping figure Figure 68. The exported marker regression report as displayed in text format

8 Page 4 List of Figures

9 Basic QTX functions : Introduction and definitions Page 1 Basic QTX functions Introduction and definitions Figure 1. A QTX dataset window showing the number of chromosomes, number of loci per chromosome, and number of progeny. A dataset contains all information related to a genetic cross or a set of recombinant inbred lines. Within a dataset are four types of objects: loci, progeny, genotypes and trait values. A locus is a location within a chromosome at which genotypes have been recorded; a chromosome is the next hierarchical arrangement within QTX: a collection of a group of loci. A chromosome in QTX will not necessarily contain a collection of loci that are physically linked by being found on the same chromosome; unrelated or unknown genotypes may be grouped together in a single chromosome in order to distinguish them from the other loci. Trait values, which are linked to genotypes by QTL mapping, are the observed values for a quantitative trait. They represent the interacting effects of alleles at more than one locus. Trait values are entered into QTX for each individual progeny member. Datasets Trait values

10 Page 2 Basic QTX functions : Introduction and definitions Figure 2. The Stat (statistics) view of chromosome 1 from the previous dataset. Progeny Genotypes Progeny are the individual members of a dataset who display trait values and genotypes at various loci; the range of possible genotypes will be dependent on what type of cross produced the progeny. Genotypes are the inferred alleles at particular marker loci. The observed genetic state at a locus is, strictly speaking, a phenotype. Possible genotypes are inferred from the phenotype. However, to make a clear distinction between quantitative trait values and marker genotypes, we will use the term phenotype only for quantitative trait values. Figure 3. The Geno (genotype) view of chromosome 1 from the previous dataset.

11 Basic QTX functions : Selecting a dataset Page 3 Selecting a dataset There are three different ways in which a dataset may be selected in order to allow a user access to QTX functions: 1. By opening a dataset window for a dataset file that is currently open; 2. By opening a dataset file that is not currently open; 3. By creating a new dataset. Opening a dataset window Select Set [the dataset name] from under the Set menu. This will open the dataset window if it is closed, or bring it to the front if it is open. It will also make this set the active set. This dataset s window is active. This dataset is not active, though the dataset file is open. Figure 4. The Set menu in QTX listing datasets with active and inactive windows. Opening a dataset file Select File Open or press Command-O (Control-O for Windows) to open an existing dataset; or select Open to bring up a dialog box from which you may select the folder in which the desired dataset resides.

12 Page 4 Basic QTX functions : Selecting a dataset Creating a new dataset 1. Choose Set New to open the Set Edit Window (see Creating a new dataset (page 6)); or 2. Choose File Import to import data into QTX from text, MapMaker, trait text, or map files (see Importing files (page 22)); or 3. Combine progeny from between two or more different datasets into one new dataset by selecting individual loci and/or chromosomes and dragging them between datasets; or by cutting and pasting the loci and chromosomes into different datasets. Once a dataset is chosen as described above, or created as described in the next section, it becomes the active dataset. The majority of functions in QTX will act on a selected chromosome once a dataset has been opened. To select a chromosome and permit the activation of other options, simply click with the mouse on the desired chromosome in the dataset window. The chromosome highlighted then becomes the active chromosome.

13 Basic QTX functions : Opening, closing, and saving current datasets Page 5 Opening, closing, and saving current datasets Once a dataset file has been opened as described under Selecting a dataset (page 3), the contents of the entire dataset are held in random access memory (RAM). If no changes are made during the time in which a dataset is open and active, no alert box will appear asking you to save the dataset when you close the dataset window using the Close (Command-W) command, or when you quit the QTX program using the Exit (Command- Q) command. Figure 5. The QTX window menu with the Close command highlighted. However, if changes are made to a dataset and the dataset window is closed, the dataset file remains open with the included changes. Subsequently, an alert box will be generated to confirm whether changes should be saved or not if the File Close or File Quit commands are used. In order to save those changes, the set name must be selected from under the Set menu and Save (Command-S) selected, or you will be prompted to save the changes as described above when quitting the QTX program. If you wish to save changes to a dataset in a separate file from the original or source dataset file, select Save As... from the File menu and rename the dataset in the dialog box. New data added to a dataset but not yet saved could be lost if the QTX program is forced to quit. Therefore, it is recommended that you always try to use the Save command after every significant change.

14 Page 6 Basic QTX functions : Creating a new dataset Creating a new dataset When you initially create a dataset, there are three catagories of data that need to be entered into QTX: 1. A name for the new dataset; 2. The number of progeny in the dataset; 3. Abbreviations to represent progeny genotypes at selected loci. QTX dataset names are different from file names; the file name appears first in the header window, and the set name appears in parentheses. You may want to keep the same set name, but use different file names to indicate the relationship between progeny sets. Figure 6. A dataset window header. You may show through names which dataset files are related to each other by giving the dataset a name that indicates a dataset type and a special name to the files that specifies the particular set of progeny included in a dataset. Once you have decided on dataset and file names and have compiled the genotypes for your dataset, open the QTX application and complete these steps: 1. Choose Set New from the menu bar. 2. The Set Edit window will be displayed in the active window in the center of your screen. The Set Name field will be highlighted. Type in the new dataset name, which can consist of up to 15 alphanumeric characters.

15 Basic QTX functions : Creating a new dataset Page 7 Dataset name is changed here Number of progeny is changed here Default progeny names Default genotype abbreviations Figure 7. The Set Edit dialog box. 3. Press the tab key if you know the number of progeny to be included in your dataset; the cursor will appear in the # Progeny field. The default number of 16 can be overtyped. Click Apply. 4. At this time, you will also be able to edit the progeny names and genotype abbreviations that you wish to use for your dataset. Make any edits that are necessary by clicking in the progeny names area or genotype abbreviations areas. You can also access the genotype abbreviations by hitting the tab key five times or the progeny names by hitting the tab key fourteen times from the start position in the Name field. Click OK. The New Dataset Dialog window will close, and a regular dataset window featuring the header Untitled (name for dataset file) will remain on the desktop. Default file name before step 6 is completed Dataset set name (set field entry) Figure 8. A new dataset window after setup.

16 Page 8 Basic QTX functions : Creating a new dataset 5. To save the dataset file on your hard drive, choose File Save or File Save As. A standard file save dialog box will appear, allowing you to choose both the name and folder into which the dataset file is to be stored on your hard drive. In the process, Untitled as the file name will be replaced by whatever name is typed into the dialog box entry field in this step. 6. If you quit the QTX program without saving the new dataset as described in steps 4 and 5, an alert box will appear asking if you wish to save the dataset or discard it.

17 Basic QTX functions : Entering marker genotype data Page 9 Entering marker genotype data 1. Open a previously created dataset by selecting File Open or Command-O from within the QTX application, and selecting the name of the dataset. The dataset window will be visible on the desktop. 2. In order to add loci to your dataset, they must first be associated with a chromosome. To add a chromosome, choose Chr New from the menu bar. 3. A new chromosome dialog box will appear. The cursor will be located in the Name field; type in the name or number that you wish to assign to the chromosome. If you know the map position of the first locus at this time, you can press the tab key to advance the cursor to the Map Offset field and enter it. Figure 9. A new chromosome dialog box. 4. Click OK. The new chromosome dialog box will close, and a chromosome entry will now appear in the dataset window. 5. Highlight the new chromosome by clicking it once with the mouse in the dataset window. This action will activate the Locus menu. 6. Choose Locus New or type Command-L; the new locus dialog box will appear with the cursor in the Name window. Enter a name for the locus by overtyping the default NoName entry; the name is limited to 15 alphanumeric characters.

18 Page 10 Basic QTX functions : Entering marker genotype data New locus names are entered here References are entered here Notes are entered here Aliases are entered here Progeny names Genotype abbreviations (unknown or "U" by default) Figure 10. A new locus dialog box. 7. Press the tab key once to advance to the alias window. An alias is a former or alternative name of 15 or fewer alphanumeric characters. 8. Press the tab key again to advance to the reference window. The reference section was originally designed to contain a bibliographic reference. 9. Press the tab key a third time to move the cursor to the note window, which is designed to contain any other information you wish to attach to a locus aside from the reference. 10. If you do not wish to give the locus an alias or attach a reference or note, press the tab key four times to advance to the genotype window. 11. The cursor will be positioned below the first progeny individual s name. Enter genotype abbreviations as designated in the new dataset window;you may type either upper or lower case as QTX will automatically convert to the upper-case letters if necessary. You may skip progeny individuals if necessary by using the tab or right arrow keys to move to a subsequent blank. 12. When your data entry is finished, click OK. The new locus dialog box will be closed, and the l heading in the dataset window will be updated to reflect the addition of a new locus. 13. Save the dataset.

19 Basic QTX functions : Correcting marker genotypes Page 11 Correcting marker genotypes Once genotype data is entered into the QTX application, you will want to check it for any possible transcription errors before completing testing for QTLs in order to ensure the most accurate results. You may print data from the chromosome window to proofread it, or you may view it directly on screen. In either instance, once you have established that errors are present in the dataset, use the following procedure to correct errors: 1. Open the dataset that you wish to edit: make sure that the popup menu in the dataset window is not set to "Map". 2. Double-click a chromosome in the dataset window to open the chromosome window. 3. Click the name of the desired locus in the chromosome window, or double-click the locus name to select it. The entire row of genotypes for that locus will be highlighted. 4. Choose Locus Edit from the menu bar. The locus edit dialog will be opened. The genotype window, with progeny names and genotypes Figure 11. A new locus dialog. 5. The cursor will be positioned in the Name field. To bring the cursor down to the genotype window, either press the tab key five times to advance to the first entry, or click directly on a genotype entry. 6. As you retype entries, you may move back and forth between progeny by mouse clicks, using the tab key, or using the arrow keys.

20 Page 12 Basic QTX functions : Correcting marker genotypes 7. Once corrections are complete, click OK. The locus edit dialog box will be closed. 8. Save the dataset. Alternatively, you can also use the next procedure to change marker genotypes. 1. Open the dataset that is to be edited. Make certain that the window view is set to "Geno". 2. Double-click on a chromosome to open the chromosome window. 3. Option-click on a genotype; the cursor will become a circle, allowing you to cycle through genotype options as you hold down the option key and click the mouse button. 4. When you reach the desired genotype, save the dataset.

21 Basic QTX functions : Entering trait phenotype data Page 13 Entering trait phenotype data Trait phenotype data consists of the values generated for a particular quantitative trait. QTX allows you to set up and save trait names for a particular dataset, even if you have not already obtained all of the values for a trait, so you may go back and fill in missing trait values later. The number of progeny previously entered into either the new dataset dialog or the new progeny dialog will be represented in the New Trait Dialog when it is opened in the following procedure. Keep in mind that if trait values are generally greater than 1000 or less than 0.001, they should be scaled so that they are within that range. Otherwise, QTX may have problems analyzing or displaying your data. 1. Open or create a new dataset as described in Creating a new dataset (page 6), if a dataset is not already open. 2. Choose QT New to open the new trait dialog. Enter trait names here Aliases are entered here References are entered here Trait values are entered here for parents Notes are entered here Trait values are entered here for progeny Figure 12. A new trait dialog. 3. The cursor will be active in the Name field. This is the only field that must be completed in order to save a trait. If this is all you want to save in the dataset for a trait value at this time, skip to step If you wish to enter information in the Alias, Reference, or Note fields, press the tab key to advance the cursor. If you wish to skip to the trait value fields, press the tab key four times or click with the mouse in the desired value fields. You may use the tab

22 Page 14 Basic QTX functions : Entering trait phenotype data key to advance between the maternal, paternal, heterozygote, and progeny trait fields; or use the right arrow key or the mouse to move between entries in the progeny value fields. 5. The maternal, paternal, and heterozygote trait value fields will accommodate a maximum of fifteen digits, or fourteen digits and one decimal point; and the progeny trait value fields will accommodate a maximum of nine digits. Once a decimal point has been inserted into a progeny field value, only digits up to the thousandths place will be saved. 6. When your data entry is complete, click OK. 7. Save the dataset.

23 Basic QTX functions : Adding progeny to datasets Page 15 Adding progeny to datasets Progeny may be added to a dataset in two ways: 1) as new additions to a current dataset; or 2) as transfers from one dataset to another. Adding new progeny to a current dataset 1. Open the dataset to which progeny are to be added. 2. Select Progeny New from the menu bar. 3. A new progeny dialog box will appear foremost on the screen. The number assigned to the new progeny individual as an identifier will appear in the top field. Default progeny name Number of progeny to be added Figure 13. A new progeny dialog. 4. If you wish to add more than one progeny member to your dataset, press the tab key twice. The cursor will be advanced to the # field; type in the number of progeny to be added. (This step automatically numbers the additional progeny from the name of the last saved progeny in the dataset.) 5. Click OK. The new progeny dialog box will close, and the p field in the heading of the dataset window will be updated with the new number of progeny in the dataset. Copying progeny between datasets 1. Open dataset windows for two datasets: 1) the source set from which progeny are to be copied; and 2) the destination set to which progeny are to be pasted.

24 Page 16 Basic QTX functions : Adding progeny to datasets Figure 14. The dataset windows for Import 1, the destination dataset, and Import 2, the source dataset. 2. Open a genotype window in the source set. Figure 15. The genotype window for chromosome 1 in the source dataset, Import Select a progeny member or a range of progeny to be copied. To select one progeny member, simply click on the progeny name above the genotype listings. To select a range of progeny, click on the progeny name of either the first or last progeny member in the range, then hold down the Shift key and click on the other endpoint progeny in the range. To revise a progeny range, hold down the Shift key and click on the progeny member within the range that you wish to designate as the revised endpoint of the range. Discontinguous ranges of progeny cannot be selected all at once; you will have to individually select and copy progeny in those cases.

25 Basic QTX functions : Adding progeny to datasets Page 17 Figure 16. Progeny number 3 in the source dataset is currently selected. Figure 17. The range of progeny numbers 3-7 is selected. 4. Choose Copy Progeny from the Edit menu. 5. Open a genotype window in the destination set. If you wish to place the pasted progeny precisely, select a progeny member in the destination set to the right of the desired insertion point in the dataset. The pasted progeny will be inserted before the selection. 6. Choose Paste Progeny from the Edit menu. 7. If you wish to remove the pasted progeny permanently from the source dataset, click on the source dataset window to select it, then choose Clear Progeny from the Edit menu. 8. Save the destination dataset.

26 Page 18 Basic QTX functions : Creating a custom progeny order Creating a custom progeny order Creating a custom progeny order can be useful when entering missing data, as all of the progeny without genotypes at a locus may be grouped together at the far left or right of a dataset, regardless of how the progeny are ordered or named. (See the Progeny Orders Dialog section in the main manual for more detailed information on each of the sorted progeny options). 1. Open a dataset within which you wish to move progeny. 2. Select a chromosome from within the open dataset, either by selecting the chromosome in the dataset window by clicking it with the mouse, or by opening a chromosome window. 3. Choose Window Progeny Orders to activate the progeny orders dialog. 4. Select the Internal listing in the dataset orders window. Figure 18. The progeny orders dialog on the left shows the internal progeny order about to be copied, and the dialog on the right shows the internal progeny order after being copied. 5. Click the Copy button located in the lower left-hand corner. 6. An Internal copy listing will appear in the dataset orders window. Click twice to highlight the name if you wish to rename the order, and overtype.

27 Basic QTX functions : Creating a custom progeny order Page 19 Figure 19. The default new progeny order name is highlighted for overtyping. 7. Close the Progeny Orders window. (If the window is not closed before the chromosome window is opened, the new progeny order that you just named will appear in the pull-down progeny order as "Internal copy", the default name.) 8. Double-click on the previously selected chromosome to open it. 9. In the upper left-hand corner of the chromosome window, change the pull-down progeny order selection from Internal to the name of the new order that you just created. (To modify the order of progeny, the order selected in this step must always be something other than the default Internal order.)

28 Page 20 Basic QTX functions : Creating a custom progeny order Figure 20. A chromosome showing the new order activated in the Progeny Orders window after being added to the dataset. 10. Click once on the numbers or names of progeny individuals that you wish to move, wait briefly, then click and hold the mouse button. The cursor will change to a hand. Now you can hold down the mouse button and drag the progeny to their desired locations. To select more that one continguous progeny member within the same dataset, click to select the first member in the range, then hold down the shift key and select subsequent progeny. Discontinguous progeny that you wish to move will need to be selected and moved individually.

29 Basic QTX functions : Creating a custom progeny order Page 21 Figure 21. Progeny member 1 in this dataset is selected to be moved. Figure 22. Progeny member 1 in this dataset has been moved. 11. Save the dataset. An name to the right of the listing for the selected chromosome, visible in the Xref Dataset Window, will display the name of the progeny order currently being used (no listing is present if the Internal order is currently active).

30 Page 22 Basic QTX functions : Importing files Importing files You may need to import files into QTX if you have previously saved genotype and trait data in word processing or spreadsheet programs, or in other QTL applications. QTX also allows you to import files from online genotype downloads available at the Jackson Laboratory web site, or simply to import map distances for a particular dataset. Importing genotypes from a spreadsheet file The characteristics of a spreadsheet file correctly formatted for import are shown in Import 1: 1) The first column in the spreadsheet contains the locus name with no spaces; 2) There are no empty columns between the loci names and the genotypes; 3) There are no emply rows between loci. For the process of importing genotypes into QTX, your data files need only to contain two pieces of information: 1) locus names; and 2) genotypes. The locus name must not contain any spaces (e.g., Locus1 instead of Locus 1). If progeny names are included, as in the Import 2 file shown in Figure 24, the names cannot include leading tabs or spaces. Figure 23. A spreadsheet file formatted correctly for import that contains loci names and genotypes. Data sorted into chromosomes and carrying progeny names should have the additional formatting shown in Import 2: 4) The progeny names are in the first row of the spreadsheet, and empty cells are optional; 5) The first column in the spreadsheet contains the chromosome names with no spaces; 6) There are no empty rows between chromosomes or loci. Figure 24. A spreadsheet file formatted correctly for import that contains loci names and genotypes, plus chromosome and progeny names. To be imported, one copy of your source file must be saved as tab-delimited text, rather than in spreadsheet format. (You should still keep a copy of your source data saved in spreadsheet format if you anticipate making more entries or changes to your source file itself after the initial QTX analysis.)

31 Basic QTX functions : Importing files Page 23 The easiest way to format genotype data in a spreadsheet file is to enter each individual genotype for a particular locus in a separate cell across one row. The locus name should be in the first column, and the genotypes should follow in the subsequent columns, with no blank columns left between locus names and genotypes. 1. Save the spreadsheet file as text. 2. Choose File Import Text from the menu bar in the QTX application. 3. The Set Edit dialog will be displayed in the active window in the center of your screen. The Set Name field will be highlighted. Type in the new dataset name, which can consist of up to 15 alphanumeric characters. For an illustration of this dialog, see Creating a new dataset (page 6). 4. Press the tab key to move the cursor to the # Progeny field. The default number of 16 can be overtyped. Click Apply. 5. At this time, you will also be able to edit the progeny names and genotype abbreviations that you wish to use for your dataset. Make any edits that are necessary, and click OK. Genotype abbreviations must match those used in the file (including the case). The Set Edit dialog will close, and a standard file open dialog will appear on the desktop. Choose the name of the text file to be imported and click Open. 6. The import text dialog will now appear on the desktop to allow you to specify the types of information included in the text file. Check the buttons that correspond to the information included in the text file that is being imported, and deselect any of the default settings that do not correspond to what is included in the text import file. Note that the Dataset and Chr checkboxes control the inclusion of all the indented items under them. The Between Items field should have the Tab item checked, the Between Records field should have the Return item checked, and the Between Genotypes field should have the tab item checked in order for the import process to be completed. Click OK when the settings are correct.

32 Page 24 Basic QTX functions : Importing files Figure 25. The correct import settings for the Import 1 file, containing loci names and genotypes. Figure 26. The correct import settings for the Import 2 file, containing chromosome, loci, and progeny names plus genotypes. 7. A new dataset window will appear on the desktop when the import

33 Basic QTX functions : Importing files Page 25 process is complete; the window header will read Untitled (name you just gave dataset). Figure 27. The dataset windows for the Import 1 and Import 2 files. 8. To save the dataset file on your hard drive, choose File Save. If you wish to give the dataset file a different name, go to step A standard file save dialog box will appear, allowing you to choose both the name and folder into which the dataset file is to be stored on your hard drive. In the process, Untitled as the dataset file name will be replaced by whatever name is typed into the dialog box entry field in this step. 10. If you quit the QTX program without saving the new dataset as described in steps 7 and 8, an alert box will appear asking if you wish to save the dataset or discard it. When troubleshooting import dataset files: 1) Check the dataset windows to see if the correct number of loci and progeny were imported; 2) If there are errors, and your file format is correct as previously described, go back to your source file and check for extra spaces. If there is an extra space in the beginning or end of a cell, whether the entry is a locus, chromosome, or progeny name or genotype, QTX will interpret the space as a data entry; 3) If there are no extra spaces in the source file, check the Import dialog box to be certain that the correct settings were selected, as shown previously. Importing trait values from a spreadsheet file To import trait values into QTX, your data files need only to contain two pieces of information: 1) trait names; and 2) trait values. The trait name must not contain any spaces (e.g., Trait1 instead of Trait 1). Figure 28. A spreadsheet file correctly formatted for import containing trait names and values. To import files, save a copy of your spreadsheet file as tab-delimited text, rather than in spreadsheet format. The easiest way to save trait value data in a spreadsheet file is by entering the trait value name in the first column, followed by each individual trait value in a separate cell across one row, then saving a copy of the file

34 Page 26 Basic QTX functions : Importing files for your import as text. Use "x" or some other non-numeric character for missing values. You must have a value or an "x" for each progeny individual in the set that will import the file. If you wish to retain the formatting of the source file, save the tab-delimited text file under a different name. 1. Open the dataset whose trait values you wish to import. 2. Choose File Import Trait Text from the menu bar. 3. A standard file open dialog will appear on the desktop. Choose the name of the file containing the trait text and click Open. 4. A trait window will appear on the desktop when the import process is complete; the window header will match the name of the dataset. Figure 29. The trait window following the successful import of a trait value file. 5. To save the trait data with the dataset, choose File Save. Importing genotypes from a word processing file To import genotypes into QTX, your data files need only contain two pieces of information: 1) locus names; and 2) genotypes. The locus name must not contain any spaces (e.g., Locus1 instead of Locus 1) and should be followed by its corresponding genotypes all in a row on the same line, with tab characters separating the locus name from the initial genotype, and the genotypes separated from each other by either no spaces, space, or tab characters. A hard line return should separate loci from each other. If your import file includes progeny names, as in the Import 6 file shown in Figure 31, there should be no leading tabs or spaces as part of the names.

35 Basic QTX functions : Importing files Page 27 Figure 30. Import 8, a correctly formatted word processing file for import containing loci names and genotypes. The characteristics of a word processing file correctly formatted for import are shown in Import 8: 1) The first column contains the locus name with no spaces; 2) There is a tab character between the loci names and the genotypes; 3) There are no empty rows between loci; 4) The genotypes have no spaces separating them (you can also use space or tab characters to separate genotypes). If progeny names are part of your word processing file, as shown in Import 6, there is no need to leave extra spaces to the left of the progeny names. Figure 31. Import 6, a correctly formatted word processing file for import containing progeny and loci names in addition to genotypes. To import files, save a copy of the source file as text. If you wish to retain the formatting of the source file for future editing, save the text file under a different name. Options in the import dialog box will allow you to specify whether space, tab, or no characters separate the genotypes. 1. Choose File Import Text from the menu bar of the QTX application. 2. The Set Edit dialog will be displayed in the active window in the center of your screen. The Set Name field will be highlighted. Type in the new dataset name, which can consist of up to 15 alphanumeric characters. 3. Press the tab key; the cursor will appear in the # Progeny field. Overtype the default number of 16 with the number of genotypes each locus has. Click Apply. 4. At this time, you will also be able to edit the progeny names and genotype abbreviations that you wish to use for your dataset. Make any edits that are necessary, and click OK. The Set Edit dialog will close, and a standard file open dialog will appear on

36 Page 28 Basic QTX functions : Importing files the desktop. Choose the name of the text file to be imported and click Open. 5. The import text dialog will now appear on the desktop to allow you to specify the types of information included in the text file. The Dataset and Chr checkboxes control the items indicated below each of them. Check the buttons that correspond to the information included in the text file that is being imported, and deselect any of the default settings that do not correspond to what is included in the text import file. Note that the Dataset and Chr checkboxes control the inclusion of all the indented items under them. The Between Items field should have the tab or Space item checked, the Between Records field should have the Return item checked, and the Between Genotypes field should have the tab or Space item checked in order for the import process to be completed. Click OK when the settings are correct. Figure 32. The correct import settings for Import 6, the file containing progeny and loci names in addition to genotypes. 6. A new dataset window will appear on the desktop when the import process is complete; the window header will read Untitled (name you just gave dataset).

37 Basic QTX functions : Importing files Page 29 Figure 33. The dataset windows for the Import 8 and Import 6 files. 7. To save the dataset file on your hard drive under the same name given to the dataset, choose File Save. 8. A standard file save dialog box will appear, allowing you to choose both the name and folder into which the dataset file is to be stored on your hard drive. In the process, Untitled as the dataset name will be replaced by whatever name is typed into the dialog box entry field in this step. 9. If you quit the QTX program without saving the new dataset as described in steps 4 and 5, an alert box will appear asking if you wish to save the dataset or discard it. When troubleshooting import dataset files: 1) Check the dataset windows to see if the correct number of loci and progeny were imported; 2) If there are errors, and your file format is correct as previously described, go back to your source file and check for extra spaces. If there is an extra space in the beginning or end of a cell, whether the entry is a locus, chromosome, or progeny name or genotype, QTX will interpret the space as a data entry; 3) If there are no extra spaces in the source file, check the Import dialog box to be certain that the correct settings were selected, as shown previously. Importing trait values from a word processing document To import trait values into QTX, your data files need only contain two pieces of information: 1) trait names; and 2) trait values. The trait name must not contain any spaces (e.g., Trait1 instead of Trait 1) and should be followed by its corresponding trait values all in a row on the same line, with tab characters separating the trait name from the initial trait value, and the values separated from each other by either space or tab characters. A hard line return should separate traits from each other. Use "x" or some other non-numeric character for missing values. You must have a value or an "x" for each progeny individual in the set that will import the file. To import files, save a copy of the source file as text. If you wish to retain the formatting of the source file for future editing, save the text file under a different name. Options in the import dialog box will allow you to specify whether space, tab, or no characters separate the trait values. 1. Save a copy of the word processing document as a text file.

38 Page 30 Basic QTX functions : Importing files Figure 34. Import 6, a correctly formatted word processing file for import containing trait names and values. 2. Start the QTX application. 3. Open the dataset whose trait values you wish to import. 4. Choose File Import Trait Text from the menu bar. 5. A standard file open dialog box will appear, allowing you to choose the name and location of the trait value file to be imported into the dataset. 6. A trait window will appear on the desktop when the import process is complete; the window header will match the name of the dataset. Figure 35. The trait window following the successful import of trait values from the Import 6 file. 7. To save the trait data with its associated dataset, choose File Save. Importing genotypes from a Jackson Laboratory file The Web addresses for downloads are as follows: 1. Recombinant inbred datasets may be found at

39 Basic QTX functions : Importing files Page 31 Figure 36. The Jackson Laboratory webpage from which you can download RI data. 2. Backcross and intercross datasets may be found at Figure 37. The Jackson Laboratory webpage from which you can download backcross and intercross data. The additional data in a MapManager 2.6 file, which is a tab-separated text file, may include: 1. Aliases ( simply check the "Alias" option under the Locus header in the Import Text dialog box so files containing loci with aliases import properly).

40 Page 32 Basic QTX functions : Importing files 2. Chromosome numbers (if left in the file, they must appear on every line, with no spaces; e.g., Chr1 instead of Chr 1). 3. Notes (if left in the file, they must appear on every line). In Jackson Laboratory files, the locus name should be followed by its corresponding genotypes all in a row on the same line, with a tab character separating the locus name from the initial genotype. Spaces separate the genotypes in a JAX file, and a hard line return will separate unique loci from each other. To download and import Jackson Laboratory data: 1. Select the desired dataset from the options available on the website. 2. Choose to download the dataset as MapManager 2.6 (text) or Map- Manager (v2.b). 3. Choose to save the dataset file to disk. 4. Open the file in a word processing application. Note the number of progeny and the designated genotype abbreviations. Chromosome name Locus name Genotypes Notes and references Figure 38. A downloaded Jackson Laboratory file opened in a word processing application. Once you know the number of progeny and genotype abbreviations, use the following procedure to import the file into QTX: 1. Start the QTX application. 2. Choose File Import Text from the menu bar. 3. The Set Edit dialog will be displayed in the active window in the center of your screen. The Set Name field will be highlighted. Type in the new dataset name, which can consist of up to 15 alphanumeric characters. The cursor will then move to the # of Progeny field, which can be overtyped; the number of progeny will vary depending on the dataset that you have downloaded. Click Apply. 4. At this time, you will also be able to edit the progeny names and genotype abbreviations that you wish to use for your dataset. Make any edits that are necessary and click OK.

41 Basic QTX functions : Importing files Page The Set Edit dialog will close, and a standard file open dialog will appear on the desktop. Choose the name of the Jackson Laboratory file to be imported and click Open. 6. The import text dialog will now appear on the desktop to allow you to specify the types of information included in the text file. Check the buttons as shown below. If the file is not edited, the Between Items field should have the tab item checked, the Between Records field should have the Line Return item checked, and the Between Genotypes field should have the Space item checked in order for the import process to be completed. Click OK when the settings are correct. If you do edit the file and elect to remove the chromosome names and notes, the Between settings should still be the same as shown below, but the Chr and Name boxes will be unchecked in the second group of text file items, and the Reference box will be unchecked in the third group of text file items. Figure 39. The correct import settings for a Jackson Laboratory file, as it contains references in addition to chromosome names, plus genotypes. 7. A new dataset window will appear on the desktop when the import process is complete; the window header will read Untitled (name you just gave dataset). 8. To save the dataset file on your hard drive under the same name given to the dataset, choose File Save. 9. A standard file save dialog box will appear, allowing you to choose both the name and folder into which the dataset file is to be stored on your hard drive. In the process, Untitled as the dataset name will be replaced by whatever name is typed into the dialog box entry field in this step. 10. If you quit the QTX program without saving the new dataset as

42 Page 34 Basic QTX functions : Importing files described in steps 4 and 5, an alert box will appear asking if you wish to save the dataset or discard it. Importing genotypes from a Mapmaker/QTL file To import a Mapmaker file, which will initially be in a.raw format: 1. Choose File Import Mapmaker from the menu bar. The import process will proceed automatically. 2. A standard file open dialog will appear on the desktop. Choose the name of the Mapmaker file to be imported and click Open. 3. A new dataset window will appear on the desktop when the import process is complete; the window header will read Untitled (Mapmaker dataset name). Figure 40. The dataset window of an imported Mapmaker file. 4. To save the dataset file on your hard drive under the same name given to the dataset, choose File Save. 5. A standard file save dialog box will appear, allowing you to choose both the name and folder into which the dataset file is to be stored on your hard drive. In the process, Untitled as the dataset name will be replaced by whatever name is typed into the dialog box entry field in this step. 6. If you quit the QTX program without saving the new dataset as described in steps 4 and 5, an alert box will appear asking if you wish to save the dataset or discard it. Note: The locus order in the.raw format file is usually incorrect and no loci are assigned to chromosomes. Use the Tools Make Linkage Groups command to create initial linkage groups and locus orders. These groups may not be identical to those that Mapmaker would create, but they should be nearly the same.

43 Basic QTX functions : Importing files Page 35 Figure 41. The dataset window of an imported Mapmaker file before linkage groups are set is on the left, and the dataset window after linkage groups are set is on the right. Figure 42. The Group 1 chromosome window of a Mapmaker file before linkage groups are set; loci are unlinked because they are not in the correct order. Figure 43. The Group 1 chromosome window of a Mapmaker file after linkage groups are set; loci numbers are linked because they are in a good order.

44 Page 36 Basic QTX functions : Importing files Importing map distances Map distances in QTX are not imported as independent files, but are attached to existing datasets. When map distances are imported into QTX, the data files will only contain two pieces of information: 1) locus names; and 2) map distances between loci. Requirements for the components of a map distance file are as follows: 1. Comment lines, preceded by a pound # character may be inserted at the beginning of a file; these will be ignored during the import process. 2. The locus name must not contain any spaces (e.g., Locus1 should be used as a label instead of Locus 1) and should followed by its corresponding map distance on the same line. This distance refers to distance between the locus on that line and the following locus. 3. Distances must be expressed in Morgans, rather than centimorgans. 4. If two loci are unlinked or if the distance between two loci is unknown, a series of three dashes --- should be entered instead of the map distance. 5. A tab character should separate the locus name from the map distance. 6. A hard line return should separate loci. Figure 44. A correctly formatted word processing file with map distances between loci for import. The easiest way to save map distance data in a word processing document is by entering each individual map distance for a particular locus in one row, separated from the locus name by a tab. To import map distances into QTX: 1. Open the dataset whose map distances need to be imported. 2. Choose File Import Map from the menu bar. 3. A standard file open dialog appears to permit you to choose the file containing the map distances that are to be imported. Once a file is chosen, the import process proceeds automatically without a dialog box appearing on the desktop. 4. To save the map data with the dataset, choose File Save.

45 Basic QTX functions : Importing files Page To be certain that the map distances imported correctly, you can view the map data by choosing Options Map Functions Morgan, and either Options Chromosome Map View Interval or Cumulative, then change the pull-down menu display in the upper left corner of the dataset window from Geno to Map, and double-click on the chromosome(s) into which you have imported map data. You may also select the Stat option from the pulldown window menu of the dataset for a whole dataset or a single chromosome. Figure 45. Changing from genotype view to map view in the Import 1 file to view map distances. Figure 46. The Import 1 map distances as seen in map view.

46 Page 38 Basic QTX functions : Exporting files Exporting files Exporting genotypes You may need to export files from QTX if you wish to conduct analyses of trait data in other QT applications, such as Mapmaker, QTL Cartographer, QGene, and Pseudomarker; additionally, if there are major changes or rearrangements to a dataset, you may want to export the existing data and update it before reimporting it into QTX. Genotypes and genotype-related information are exported from QTX in text file format. The Export Text dialog allows you to decide what types of data you wish to export from a dataset file. By default, the following items will be automatically included if changes are not made to the dialog selections: Figure 47. The default export text settings. To export genotypes in a text file: 1. Choose File Export Text from the menu bar. 2. A standard file save dialog box will appear, allowing you to choose both the name and folder into which the export file is to be stored on your hard drive. 3. The export text dialog will now appear on the desktop to allow you to specify the types of information included in the text file.

47 Basic QTX functions : Exporting files Page 39 Highlight the appropriate boxes that correspond to the information to be included in the text file that is being exported, and deselect others. Note that the Dataset and Chr checkboxes control the inclusion of all the indented items under them. Click OK when you are done. 4. Choose the progeny order from those available under the popup menu. 5. To view the export file, open it using a text or word processing application. Set name Chromosome name Locus name Genotypes Figure 48. The dataset window for the exported Import 1 genotype file is shown above, and the exported genotype file itself is shown below as text. Exporting trait values When you export trait values from QTX, a standard file save dialog permits you to choose the name and location to which the trait value file is to be saved, followed by an Export Text dialog that allows you to decide what types of data are to be included. The trait text will be saved after export in a simple text format with the trait names followed by the trait values. To export trait values in a text file: 1. Open a dataset that has trait values associated with it. 2. Choose File Export Trait Text from the menu bar. Choose the progeny order from those available in the popup menu. 3. A standard file save dialog box will appear, allowing you to choose both the name and folder into which the export file is to be stored on your hard drive. 4. To view the dataset file, open it using a text or word processing application.

48 Page 40 Basic QTX functions : Exporting files Figure 49. An exported trait value file viewed in text format. Exporting genotypes for selected chromosomes/loci To export genotypes for selected chromosomes or loci, you can hide chromosomes or loci linked to a particular dataset, and then export the remaining chromosomes or loci. To hide selected chromosomes or loci: 1. Open a dataset. If you wish to hide chromosomes, leave the dataset window open. If you wish to hide loci within a chromosome, double-click on the chromosome to view loci. 2. Select by clicking in the dataset or chromosome window either the chromosome(s) and/or locus (loci) you wish to hide. 3. Select Chr Hide or Locus Hide. 4. Repeat steps 2 and 3 to hide all of the objects within a dataset that you want to remove from your export dataset. 5. Save the dataset. Once you have set up and hidden the objects in the dataset: 1. Choose File Export Text from the menu bar. 2. A standard file save dialog appears to permit you to choose the name and location to which the file containing genotypes is to be saved. 3. The export text dialog will now appear on the desktop to allow you to specify the types of information you wish to include in the text file. Highlight the appropriate boxes that correspond to the information you wish to include in the text file that is being exported, and deselect any of the default settings that do not correspond to what you wish to include in the text export file. Note that the Dataset and Chr checkboxes control the inclusion of all the indented items under them.click OK when you are done.

49 Basic QTX functions : Exporting files Page 41 Figure 50. The default export file settings for a genotype file. 4. To view the export file, open it using a text or word processing application. Exporting genotypes for selected progeny To export genotypes for selected progeny you can create a progeny order, and then remove progeny that you do not wish to export from the order. To create a progeny order and remove progeny: 1. Open a dataset. Click on any chromosome within the dataset to select it and activate the standard options for progeny order creation. 2. Under the Window menu, select the Progeny Orders option. The progeny orders dialog window will be opened. 3. Click once to select the Internal order from the orders list. 4. Click Copy. 5. The copy will be named Internal copy by default. To rename the order, double-click on Internal copy and overtype. If you do not wish to rename the order, proceed to step Click once on the chromosome window to select it, then click on the order listing in the upper right corner, which will be Internal by default, and select the new order name. 7. Click once on the numbers or names of progeny individuals whom

50 Page 42 Basic QTX functions : Exporting files you wish to remove from the order. To select more that one continguous progeny member within the same chromosome, click to select the first member in the range, then hold down the shift key and select subsequent progeny. Discontinguous progeny whom you wish to remove from the order will need to be selected and removed individually. 8. Select Progeny Remove From Order. Progeny members that were selected will no longer be visible. Figure 51. A selected progeny individual in the chromosome window. 9. Repeat steps 7 and 8 to remove all progeny that you do not wish to export from your export dataset. 10. Save the dataset. Once you have set up and saved the progeny labels in the dataset: 1. Choose File Export Text from the menu bar. 2. A standard file save dialog then appears to permit you to choose the name and location to which the genotype file is to be saved. 3. The export text dialog will now appear on the desktop to allow you to specify the types of information you wish to include in the text file. Choose the progeny order you have just created from the popup menu. Highlight the appropriate boxes that correspond to the information you wish to include in the text file that is being exported, and deselect any of the default settings that do not correspond to what you wish to include in the text export file. Note that the Dataset and Chr checkboxes control the inclusion of all the indented items under them. Click OK when you are done. 4. To view the export file, open it using a text or word processing application.

51 Exporting Mapmaker/QTL files Basic QTX functions : Exporting files Page 43 When you export files from QTX into Mapmaker, you have the option of saving chromosomes in a particular dataset as individual files, or the entire dataset as one file. A Mapmaker/QTL export dataset will contain the date and time it was created, as well as: 1. Cross type. 2. Number of progeny. 3. Number of loci. 4. Number of genotype code symbols. 5. Symbol for representing unknown genotypes. 6. Locus names. 7. Genotypes. To export a Mapmaker file: 1. Choose File Export Mapmaker from the menu bar. 2. A dialog box will appear to allow you to select the options necessary to export the desired data. Include hidden chromosomes and Include hidden loci, when checked, allow for the export of all genotypes. Prompt for all file names, when checked, allows you to specify file names, which may be convenient when you are exporting Mapmaker files to a location where other exported Mapmaker files are stored. Save as single file, when checked, allows multiple chromosomes to be saved into one Mapmaker file. Figure 52. The control dialog for exporting Mapmaker files. 3. A standard save file dialog box will appear on the desktop when the export process is complete; the default file name will be Chr 1

52 Page 44 Basic QTX functions : Exporting files Exporting Cartographer files [or individual chromosome names/numbers if you chose to export the dataset as individual chromosome files]. 4. Choose the desired filename and click Save. When you export QTX files into Cartographer, two data files will be created. The first file will be a marker map information file, which is named by default "map.inp". The information contained within the exported map file includes: 1. Mapping function. 2. Units of measurement for map distances. 3. Number of chromosomes. 4. Maximum number of loci per chromosome. 5. An indicator if locus names are present. 6. Locus names. 7. Map distances. The second file type created for a Cartographer export is a marker and trait genotype information file, which is named by default "cross.inp". The information contained within the exported cross file includes: 1. Cross type. 2. Number of traits. 3. Sample size (number of progeny). 4. An indicator that locus names are case sensitive. 5. A translation table of genotype abbreviations. To export from QTX into Cartographer: 1. Choose File Export Cartographer from the menu bar. 2. A standard save file dialog box will appear on the desktop when the first half of the export process is complete; the default file name will be map.inp as it contains all of the mapping information for the dataset.

53 Basic QTX functions : Exporting files Page 45 Figure 53. The file save dialog showing the default filename for a Cartographer export map file. 3. Choose the desired filename and click Save. 4. A standard save file dialog box will appear on the desktop when the export process is complete; the default file name will be cross.inp as it contains all of the genotypes for the dataset. Figure 54. The file save dialog showing the default filename for a Cartographer export genotype file. 5. Choose the desired filename and click Save. Exporting map distances Map distances in QTX are exported as text. You may choose to export all map distances in a particular dataset, or for only one chromosome. You can also select if you wish to export all map distances, or only user-defined map distances. Map distance data will be saved in a text file with each individual map distance for a particular locus in one row, separated from the locus name by a tab. To export map distances from QTX: 1. Open the dataset whose map distances you wish to export. If you wish only to export the map distances from one chromosome, select that chromosome in the dataset window. 2. Choose File Export Map from the menu bar.

54 Page 46 Basic QTX functions : Exporting files 3. An alert box will appear to allow you to choose to export all map distances, or only user-defined map distances. Click the appropriate button. Figure 55. The alert that appears if a chromosome is selected; in this case, Chr 4. Figure 56. The alert that appears if no individual chromosomes are selected. 4. A standard file save dialog then appears to permit you to choose the name and location to which the map distances file is to be saved; the default file name will be derived from the dataset name. Click the Save button when you have made your desired selection. Figure 57. The file save dialog showing the default filename for an export map file. 5. To view the map distances file, open it in a text or word processing application.

55 Basic QTX functions : Exporting files Page 47 Figure 58. An exported map distances file displayed in text format. Exporting into QGene QGene data will be saved in two separate files; the first file contains the locus names and corresponding map distances, and the second file contains the genotype data. To export from QTX into QGene: 1. Open the dataset that you wish to export into the QGene format. 2. Choose File Export QGene from the menu bar. 3. A standard file save dialog then appears to permit you to choose the name and location to which the map distances file is to be saved; the file name will be derived from the dataset name. Click the Save button after you have either accepted the default filename or revised it. Figure 59. The file save dialog displaying the default filename for an export QGene map file. 4. A standard file save dialog then appears to permit you to choose the

56 Page 48 Basic QTX functions : Exporting files name and location to which the genotype file is to be saved. Click the Save button after you have either accepted the default filename or revised it. Figure 60. The file save dialog displaying the default filename for an export QGene genotype file. 5. To view either of the two QGene files, open them in a text or word processing application. Figure 61. A QGene export map file in text format. Figure 62. A QGene exported genotype file in text format.

57 Exporting into Pseudomarker Basic QTX functions : Exporting files Page 49 Exported Pseudomarker data will be saved in a single file. To export from a QTX dataset into a Pseudomarker file: 1. Open the dataset that you wish to export into Pseudomarker format. 2. Choose File Export Pseudomarker from the menu bar. 3. A standard file save dialog then appears to permit you to choose the name and location to which the export file is to be saved; the default file name will be Pseudomarker text. Click the Save button after you have either accepted the default filename or revised it. Figure 63. The file save dialog displaying the default filename for an export Pseudomarker file. 4. To view the Pseudomarker file, open it in a spreadsheet, text, or word processing application.

58 Page 50 Basic QTX functions : Exporting files Figure 64. An exported Pseudomarker file displayed in text view. Exporting report window contents QTX allows you to export the contents of report windows as text, which permits you to edit the text of the report, which is saved separately from the QTX file, so the original dataset is not altered. This feature is activated when a report window is frontmost, including report windows from marker regression, interval mapping, permutation testing, and quick testing. By using this feature, you can save individual reports for future use and comparison with others. The only type of QT report window that cannot be saved as text is the interval mapping figure linked to the interval mapping report; the figure is automatically saved as a bitmap file by QTX when exported. To export a report window: 1. Open a dataset. 2. Select one of the five options from under the QT menu that generate reports: Marker Regression, Interval Mapping, Interaction, Permutation, or Quick Test. 3. Change settings as necessary in the report dialog and generate the report.

59 Basic QTX functions : Exporting files Page 51 Figure 65. A marker regression report window. 4. Choose File Save Window from the menu bar. 5. A standard file save dialog then appears to permit you to choose the name and location to which the export text or bitmap file is to be saved. Click the Save button after you have either accepted the default filename or revised it. Figure 66. The file save dialog displaying the default filename for an exported marker regression report.

60 Page 52 Basic QTX functions : Exporting files Figure 67. The file save dialog displaying the default filename for an exported interval mapping figure. 6. To view a standard report, open the export file in a text or word processing application; to open an interval mapping figure, use a graphics program. Figure 68. The exported marker regression report as displayed in text format.