Signals Tab Features and Functionalities

3.6.1

The Signal tab contains many features with the functionalities described below (see Figure 36).

•	The Options area (on the top left area of the tab) gives a choice of 6 plot types (each data set is available for each flow), broken down as follows:

◦	Number of Wells Versus: For the well type selected (Library or Control DNA), and the flow selected, display the number of wells (y-axis) as a function of one of the following (x-axis):

▪	Raw Intensity for all key pass wells

▪	Raw Intensity (Filtered) for only filter pass (always also key pass)

▪

Signal (N-mer) equivalent of the intensity values from the Raw Intensity (Filtered) signals, converted into number of nucleotides extended in the flow (i.e. “homopolymer length”, as estimated by the basecaller). This is the default view for library wells. Unless an anomaly is present in the Signal (N-mer) plot, it is unlikely that the Raw Intensity plots will need to be viewed.

◦	Well Categories: For the signal type selected (Raw Intensity, Raw Intensity – filtered, or Signal N-Mer), display the data for the wells with the following keys:

▪	GACT (Rapid Library) TCAG (Standard library) – Use the key passed wells identified as library wells.

▪	CATG and/or ATGC (control) – Use the key passed wells identified as Control DNA wells. See Section 7.1 for details on Control DNA keys.

◦	Flows: Located below the Well categories section, the Flows selector allows the user to select a flow from the sequencing Run for viewing.

▪	Only the nucleotide and PPi or ATP flows are listed (Since signal statistics for wash flows are irrelevant, there is no “Show all” check box).

▪	After clicking in the Flows selector, the keyboard arrow keys can be used to navigate quickly up and down this list.

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Navigation and data capture buttons: All the buttons on this tab have common functions: setting and adjusting the zoom level of the main image display or allowing the user to save the data as a text file or snapshot image. See Section 3.3.4 for a description of the navigation and data capture button functions.

•	Plot display: The plot shares the common scrolling and zooming functions of the other GS Run Browser plots (see Section 3.3.3), with the following exceptions:

◦

The default scales for the x and y axes have been set to fixed values that typically provide a useful view of the data. After first clicking the Flow selector, the keyboard arrow keys can be used to quickly scan from flow to flow; this constitutes a very useful troubleshooting tool for evaluating the signal distributions.

◦	The bar widths (i.e. histogram “bin sizes”) are 100.0 for Raw Intensity plots, and 0.05 for Signal (N-mer) plots. These bar widths are fixed.

◦	When the mouse pointer is over the plot, the usual mouse tracker shows the x-axis signal value and the number of wells having that signal value, in the selected flow.

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Summary:

◦	This displays a text version of the data shown in the plot, listing the height of each bar in the plot, with zero height bars omitted.

◦	An invisible divider is present between the plot area and the well density summary table that can be dragged to adjust the part of the window allotted to these two areas.