CEQ Trace Import Format

The CEQ Trace import reads data from a fragment results text file produced by a Beckman Coulter, Inc. CEQ 2000 DNA Analysis System. CEQ is a registered tradmark of Beckman Coulter, Inc. The text file contains fragment trace data, size standard data, and information about the sample.

Since the CEQ 2000 is a capillary system, the data in the file represent the four color traces collected from one capillary during a fragment separation. Genographer, however, displays these data as though they were obtained from a lane on a gel.

The program will display the following options for importing the file:

• File type
• Color (dye)
• Size Function

To import a CEQ file into Genographer, select CEQ Trace for the file type. Then select the desired trace, D1, D2, D3 or D4, from the Color menu. Finally, select a sizing function from the Size Method menu. Note that the Size Standard selection is not used by the CEQ Trace import, so any selection here is ignored.

The program expects fragment analysis results, exported from the CEQ 2000 as a text file with the Header and Result Data options selected. These file export options were first made available in version 4.0 of the CEQ software. Files exported in this manner will have the appropriate format and data for Genographer. Attempting to import CEQ files produced with any other format will result in a Genographer file import error.

The second import option is the Color, or trace dye. The file must include trace data for the selected color; otherwise, a Genographer file import error will occur.

The program can only import one color at a time. Therefore, if multiple files are imported, they must all be imported with the same color selection. If a comparison of different color traces is desired, the same files can be imported again, using another color. This will have the effect of displaying the individual traces from one capillary in multiple, logical Lanes.

The next import option is the Size Function. The size function is used to size the lane when the lane is displayed by the program. The sizing function determines how the trace points are converted to size. See the "Lane Sizing Formulas" heading in the Program Features for information on the available sizing functions.

There is no option for the Size Standard. The standards defined in the standard.cfg file are not used by the CEQ Trace import feature. Instead the CEQ Import feature uses the size standard included in the CEQ Text file. This size standard is the one selected during the CEQ fragment analysis. It will be used by the Genographer sizing function selected during the file import, regardless of the sizing model selected during the CEQ fragment analysis. If any standards were removed during the CEQ fragment analysis, before exporting the results, they will not be available for use by Genographer.

Sample information is displayed when the mouse pointer is placed over the top of any Lane. This display has the following format: Sample name "from Lane" capillary number "in" Sample Plate Name. The capillary number will be 1 through 8, representing capillaries A through H on the CEQ 2000. The sample name and the sample plate name are the names assigned by the operator during the CEQ sample plate setup.