Paired Reads Graph report
The Paired Reads Graph report graphically displays where the mates aligned for paired reads at a given reference position. The report also graphically displays the number of reads for which the mate did not align to the reference sequence in either direction.
From left to right, the following graphs are displayed on the report:
• Opposite Direction – The Opposite Direction graph shows where both reads aligned to the reference sequence in opposite directions.
• Same Direction – The Same Direction graph shows where both reads aligned to the reference sequence in the same direction.
• One End Missed – The One End Missed graph shows the number of reads that aligned to the reference sequence at a given position without a mate.
The data points in the Opposite Direction graph and in the Same Direction graph are
color-coded as indicated in the graph Legend. The color code indicates the number of reads that aligned to the reference sequence and that had mates that aligned at the same position in either the opposite direction (the Opposite Direction graph) or in the same direction (the Same Direction graph).
color-coded as indicated in the graph Legend. The color code indicates the number of reads that aligned to the reference sequence and that had mates that aligned at the same position in either the opposite direction (the Opposite Direction graph) or in the same direction (the Same Direction graph).
By default, when the report is first generated, the report shows the data points for the entire reference region. To limit the report to show only those data points that are found within regions of interest (ROIs), select In ROI only, and then specify how to define these ROIs.
Option | Description |
|---|---|
In ROI only | • One read in ROI – Only one read within a read pair must be within the ROI for the data point to be displayed. • Both in ROI – Both reads within a read pair must be within the ROI for the data point to be displayed. |
Use BED | Use the ROIs as defined in a BED file. Click Set, and then browse to and select the appropriate BED file. Note: A BED file is a tab-delimited text file. You can upload a BED file only if the reference sequence contains chromosome information, which means that the reference sequence must be either a preloaded reference that NextGENe supplies, or a GenBank reference file that contains chromosome information. |
CDS | Use all coding exons as ROIs. |
mRNA | Use all mRNA regions, including both coding and non-coding exons, as ROIs. |
ROI | Applicable only if you have loaded project for which the ROIs have been defined in a GenBank reference file. |
Set Read Count Range | Set the range of reads that are displayed in the graphs. The default value is 0 to the maximum value for the read count range for the given dataset. If you change one or both values, then you must click the Refresh button that is displayed to the right of the Max field to update the graphs’ displays. |
The report is interactive. You can use the buttons on the report toolbar, or you can manually carry out some of the same actions.
Button | Function |
|---|---|
 | Zoom In button – Zooms in on a graph view. You can also hold down the left mouse button and draw a box from the upper left hand corner of any region in the graph towards the lower right hand corner. A box is formed around the area that is being reduced for viewing. After you zoom in on a position in a graph, you can use the Move icons to navigate the display. |
 | Zoom out button – Zooms out the graph view. You can also hold down the left mouse button and draw a box from the lower right hand corner of any region in the graph towards the upper left hand corner. Note: The magnification for zooming out is always 100%. |
 | Move Right button – Moves the displays for the Opposite Direction and Same Direction reports to the right. |
 | Move Left button – Moves the displays for the Opposite Direction and Same Direction reports to the left. |
 | Move Up icon – Moves the displays for all three graphs up. |
 | Move Down button – Moves the displays for all three graphs down. |
 | Show/Hide button – Toggles the legend display (on or off) at the bottom of the report. |
 | Report Table button – Generates and displays the Paired Reads Table Report, which tabulates the information that is displayed in the three graphs in the Paired Reads Graph report. See Paired Reads Table report. |
 | Refresh button – Resets the report display to the display that is indicated by the read count range. Note: You change the range of reads that are displayed in the graphs in the Set Read Count Range fields. The default value is 0 to the maximum value for the read count range for the given dataset. |
 | For some actions, all three graphs in the report are linked. For example, if you zoom in on a region of one graph), then the same action is carried out for the other two graphs. |