User manual PERKIN-ELMER GENESCAN ANALYSIS 3.1

[. . . ] GeneScan Analysis Software Version 3. 1 User's Manual © Copyright 1998, The Perkin-Elmer Corporation This product is for research purposes only. GeneScan, Genotyper, and Perkin-Elmer are registered trademarks of The Perkin-Elmer Corporation. BioLIMS is a trademark of Molecular Informatics, Inc. ABI, ABI PRISM and the ABI PRISM design, Applied Biosystems, GenoPedigree, PE, and PE Applied Biosystems are trademarks of The Perkin-Elmer Corporation. [. . . ] Click the arrow in the Standard column for the sample that you want to change. Pop-up menu 3 4 5 Select a size standard from the pop-up menu. Edit the peak size values by following step 7 on page 5-33 to step 9 on page 5-34. Choose Save or Save As from the File menu. You can take the following action: If you choose. . . changes are saved using a file name you specify. 5-38 Analyzing Project Files Deleting an The following procedure describes how to delete a user-defined Existing Standard standard from the GS Standards Folder so that it no longer appears in the Standard pop-up menus. The standard is permanently removed and you must re-define to use it again. To delete an existing standard: Step 1 2 3 4 Action Switch to the Finder. Locate and open the Current Standards folder. Select the definition file that you want to delete. Drag the file to the trash and empty the trash. Note You can also drag the standard to another folder for storage. Analyzing Samples To select the same standard for analysis of all samples: Using the Same Step Action Standard 1 2 If the Analysis Control window is not displayed, choose Analysis Control (z 1) from the Windows menu. Click the arrow in the Standard column heading and choose a standard file from the pop-up menu. Your menu choice applies to all fields in the column. Note Alternatively, you can choose a value from the pop-up menu, click the header to select the entire column, and choose Fill Down from the Edit menu. Pop-up menu Analyzing Project Files 5-39 Step 3 Action The pop-up menu contains the following options: Item <None> <filename> Description Apply no standard definition. Apply the size standard specified in the Data Collection software, which is embedded in the Sample file. For information on editing this file, see "Editing the Size Standard Definition" on page 5-36. custom standards that are listed at the bottom of the menu These are files that you defined and they are located in the parameters folder specified in the Folder Locations preferences. For information on setting the Folder Locations preferences, see"Defining Folder Locations" on page 5-41. Selecting Separate To apply separate size standards to selected samples, click the arrow in Standards for the Standard column for the sample that you want to change (see figure Samples below) and a pop-up menu appears. For information on using the pop-up menu, see step 3 above. Pop-up menu 5-40 Analyzing Project Files Defining Folder Locations Introduction The GeneScan Analysis Software looks in the designated folders for the: o o o Size Standard file. Matrix file. When saving one of these files for the first time, the default folder locations for saving the files are those same designated folders. Storing Matrix Store matrix files, that are intended for use by Data Collection software Files to assign to collection runs, in the ABI Folder. The ABI Folder is located in the System folder on the computer on which the Data Collection software is installed. [. . . ] separation distance Length from the wells of the gel to the read region of the gel. Also called the "WTR (well-to-read). " shark's-tooth comb Piece of mylar inserted into a gel, typically used for a sequencing run. The flat edge of the comb is used to form a well during gel polymerization. The toothed edge is inserted to form wells into which samples are loaded. [. . . ]