The Chromatogram Editor Window is displayed whenever a trace file is opened. The editor looks very similar to the Single Sequence editor with the following changes:
1. A Sequence Type indicator. This is simply an icon to indicate that the trace represents a DNA sequence. It cannot be clicked.
2. Clicking the Features tab moves to a window that contains the features table for the sequence. The sequence must be unlocked in order to make any changes. NOTE: changes here will not be saved in a chromatogram format, but WILL be saved if you choose a file format that supports GenBank-style annotations.
3. Clicking the Annotations tab view shows the Annotations tab of the sequence. The window is editable, but the chromatogram must be unlocked in order to make any changes. NOTE: the only changes here that will be saved in a chromatogram format are edits to the comment section. However, other annotations WILL be saved if you choose a file format that supports GenBank-style annotations.
4. Clicking the Map View tab displays the annotated graphic of the sequence. This is generally empty for trace files, but is supported for consistency with the Sequence Editor.
5. The "A", "C", "G" and "T" buttons allow you to show/hide the appropriate trace channel. This can be useful when attempting to interpret crowded areas of the chromatogram where two or more channels show significant signal.
6. The Raw Data displays the quality values and areas under each trace curve for each sequence residue in a tab delimited format that can be copied into Excel for additional analysis.
You can save chromatogram data in one of two basic formats:
MacVector saves chromatogram data only as SCF (Staden Chromatogram Format) version 3 files. This file format supports saving trace data, along with the sequence and comments. Any feature or annotation data other than comments will not be saved into the file. The extension ".scf" is automatically appended to saved files.
Chromatograms can also be saved in any sequence file format supported by MacVector. By default, chromatogram files are saved in SCF format. To save in a different format, choose FILE | Save As... and select the required file format using the FORMAT popup menu. When saved as a sequence file, the trace data will not be saved with the sequence. However, any features or annotations you have added to the chromatogram will be included in the new file.
The Raw Data tab shows the quality and the area under each peak for all four bases. This can be copied and pasted directly into a spreadsheet application such as Excel.