Well Flowgrams (for Wells Generating Library Reads)

3.5.2

Double-clicking the mouse in the main image area brings up the closest well’s processed flowgram, which was generated by the GS Run Processor application and is used to determine the basecalled sequence for that well. In this flowgram view, all flows are shown rather than only the flows generating the trimmed sequence. The flowgram viewer for wells producing library reads (starting with the “TCAG” or “GACT” key), is shown below (Figure 32). The flowgram viewer for Control DNA wells is described in Section 3.5.3.

Figure 32: Well Signal Flowgram Plot

Only one well flowgram window (or Control DNA well tri-flowgram window) can be open at a time; selecting the well flowgram action for another well on the main image area will replace any existing data in the well flowgram window. However, both a well flowgram window and a location or a subtraction flowgram window can be open at the same time (see Sections 3.5.2 through 3.5.5).

3.5.2.1

Well Flowgram Features and Functionalities

The well flowgram window has the following areas, with the functionalities described (see Figure 32):

•	Title bar: The window title identifies the type of flowgram window (Well Flowgram), the PicoTiterPlate Device region and the x,y location of the well, and the well’s attribute value for the currently selected category.

•	Option controls:

◦	Flowgram option: Choice of the type of flowgram signal to display:

◦	Corrected Intensity – Display the processed (“corrected”) signal intensity as computed by the GS Run Processor application.

◦	N-mers – Display each signal as an estimate of the number of bases extended at each flow (i.e., the homopolymer length).

◦	Choice of 3 plot Styles: Bars, Lines, or Lollipop. In all cases, the reagent flowed in each step is color-coded, per the legend. The lines and lollipop styles are narrower than the bar style, and will allow viewing more of a Run without scrolling.

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Navigation and data capture buttons: All the buttons in this window have common functions: setting and adjusting the zoom level of the plot display, or allowing a 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 for a description of the plot functions.

•	The default y-axis scale is set on the fly to values appropriate for visualizing the range of signals generated for the well flowgram displayed. The navigation buttons can be used to adjust this zoom level.

•	When the mouse pointer is over the plot, the mouse tracker shows the flow number, the reagent flowed, and the count/intensity for the flow under the pointer.

•	Signal legend: This area shows the colors used to display the flowgram signals on the plot; each reagent is shown in a different color.

For data sets processed with the software version 1.1.03 or earlier, the nucleotide labels of the x-axis of the well flowgrams come from the imageLog.parse file. If this file is absent (e.g. if the D_ directory has been separated from its parent R_ directory), the software will attempt to infer what the flows were. If incorrect, this can be overridden by specifying the proper data set type using the drop down menu on the Overview tab (see Section 3.4.3).