Using the Flowgrams Tab

4.14	Using the Flowgrams Tab

The term “flowgram” is defined in the Glossary and a full description of flowgram views is given in the section on the GS Run Browser, in Part B of this reference Manual.

The flowgram view as displayed on the Flowgram tab of the GS De Novo Assembler and the GS Reference Mapper (Figure 98) is most similar to the tri-flowgram view described in detail in the GS Run Browser section in that it shows 3 plots:

•	The top plot is an idealized flowgram for either:

•	the consensus sequence of the contig containing the selected read (when using the assembler) or,

•	the selected reference sequence (when using the mapper).

•	The top flowgram may include insertions of flow cycle shifts as needed to maintain the alignment to the selected read’s actual flowgram.

•	The center plot is the aligned flowgram for the selected read, including the insertions of any flow cycle shifts that may be needed to maintain the alignment to the idealized consensus flowgram.

•	The lower plot is the flow-by-flow difference between the two upper plots.

Figure 98: gsMapper Flowgrams Tab

A small green triangle indicates the flow corresponding to the base of the read on which you right-clicked when launching the Flowgrams tab view.

The Flowgram tab provides various navigation options and other features:

•	The top-left corner of the tab provides two controls that allow the user to change the display to a different read:

◦

A pull-down menu allows you to select from a list of all the reads in the contig to which the read currently displayed belongs (Figure 98), and which span the base position of the alignment that was used when initially launching the Flowgrams tab. That base position may be quickly updated by navigating back to the Alignment results tab and selecting a new alignment column (nucleotide in the sequence) by simply left-clicking in that column. Then switch back to the Flowgrams tab (by clicking on the tab). The drop down menu will be updated to include only those reads that have flowgrams and also which intersect with the new column of interest. The read previously displayed in the flowgram view will remain displayed (unless the new column of interest is not spanned by that read), but the green triangle will be updated to point to the flow corresponding to the nucleotide in the new column of interest. If the previously displayed read does not span the new column of interest, then the display will automatically go to the first read, topmost in the displayed alignment, which does span the column.

◦	The pair of buttons, “Prev” and “Next”; allows you to change the display to the previous or the next read of the contig’s multiple alignment (in the order shown in the Alignment Results tab).

•	You can also return to the Alignment Results tab and select a different read, from the alignment to the same or to any other contig.

•	The plot navigation buttons appearing to the left of the flowgram have the following functions:

	Zoom in Y – Zoom in by a factor of 1.5. For plots, this button zooms only the y-axis scale (use the Zoom to labels and Freehand zooming functions described below to zoom the x-axis).
	Zoom out Y – Zoom out by a factor of 1.5. For plots, this will zoom only the y-axis scale and, unlike most zoom operations, this will zoom out past the data limits (to allow the user to get a better perspective of the data).
	Zoom in labels – This button zooms the x-axis of the flowgram so that the nucleotide/flow characters can fit below the axis.
	Zoom fit – Fit means ‘zoom all the way out.’ On plots, scale out to the limits of the data.
	Output PNG – Save a snapshot image of the current view to disk. This will open a dialog asking for a location and filename, and then will save a PNG image file at the location specified. The saved image contains only the visible region of the plot.
	Output Text – Save a tab (.txt) or comma-separated (.csv) text file of the data for this graphic. This will open a dialog asking for the location and filename to save the file. It then saves the data, along with summary information describing where the data came from. The data for all three plot subsections is saved to one file, with white space between subsection plot data.

•	The lower panel (difference flowgram) has a separate set of zoom buttons (Zoom in Y, Zoom out Y, and Zom fit) because the scale of its Y axis (difference) is typically much smaller than that of the upper two panels.

•	A mouse tracker area that shows the values for the nucleotide flow under the mouse pointer, when you pause it over the graph area:

•	position of the nucleotide on the consensus or reference sequence,

•	name of the nucleotide, and

•	the “y” value on the plot

•	number of bases added during that flow (idealized per the consensus [assembly] or reference sequence [mapping] or observed in the read), or

•	the value of the “difference”, where bases in the read that are absent in the consensus or reference are positive differences.

•

There is also a free hand zoom function that allows you to zoom in to any area of a plot by drawing a box with the left mouse button. This function has the following unique features (not available in the corresponding GS Run Browser freehand zoom in functions) to facilitate the comparison between the three plots:

•	zooming on the consensus/reference or on the read plots will apply to the Y axis of both those plots, and the X-axis of all three plots (including the difference plot).

•	zooming on the difference plot zooms its Y axis alone, but zooms the X axis of all three plots (not shown).