![]() Figure 15-2 Trace with hidden lanes and adjusted scales You can specify the settings for trace display by going to the Window menu and choosing User Preferences and selecting Chromatogram. Note that as you do so all the contig chromatograms will move left or right, in step with the highlighted base. When you are working in a contig, if you highlight a base in the consensus line you can use the arrow keys to move through the consensus sequence. Alternately, you can use the left arrow and right arrow keys to step through the sequence trace, base by base. With the mouse button held down, you can move the slider down or up, depending on your current position within the sequence. Position your cursor on the small rectangular slider button to the right of the trace. Scrolling through a single chromatogram is simple. Figure 15-2 shows a contig with adjusted scales and hidden lanes. Below the slider are four buttons that let you hide the lanes for any or all of the traces. Below the arrows is a slider for changing the height of the trace. The arrows to the left show the orientation and relative lengths of the trimmed and untrimmed data. The lower line displays the base calls as originally imported, including the trimmed data. The upper line displays the sequence as it currently appears in the editor, including any edits you may have made. Understanding the Trace Display Above the traces are two lines of bases. When you move the cursor back into a region where there are fragments with chromatogram data, the traces will reappear. When you click the Show Chromatograms button in a region without trace data you will see a “No Chromatogram Data” message in the Contig Chromatogram window. Figure 15-1 Selected column chromatograms SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. The bases you highlighted in the contig editor will also be highlighted in the trace windows. Sequencher opens a window to display the traces (Figure 15-1). Then click the Show Chromatogram button or go to the Window menu and choose Chromatogram. Select a contig column by clicking on its base in the consensus line (Figure 15-1). This allows you to check the signal strength of any peak in conjunction with its base call and edit your data accordingly. If you are elsewhere in the contig, Sequencher selects the center-most consensus base in the contig display and displays the associated traces. If you are at the 5’ end of the contig, Sequencher selects the most 5’ base in the consensus and displays all the associated traces. Viewing chromatograms from a contig editor The Sequencher contig editor allows you to view simultaneously all chromatogram data relevant to a consensus base call. Note: Remember that even if a sequence fragment is incorporated into a contig, you can still open its editor by double-clicking the sequence name in the list at the left of the contig editor. ![]()
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