Opposite Direction/Same Direction Paired Reads reports
The Opposite Direction Paired Reads report lists all the pairs that aligned to the reference genome in opposite directions and that have a gap distance that is outside the expected range. The Same Direction Paired report lists all the pairs that aligned to the reference genome in the same direction and that have a gap distance that is outside the expected range. After you select either report option, a Filter Settings dialog box opens.
Setting | Description |
|---|---|
• Input Region Manually • Entire Reference Range | You must specify the starting position and the ending position, or you can select Entire Reference Range to include the entire reference range in the output. |
Input points of interest text file (*.txt) | There are no special requirements for uploading a comma-delimited text file. If the input text file is a comma-delimited text file, it must contain one of the following lists: • A list of specific reference locations (position number) separated by commas • A list of reference ranges (start position number - end position number) separated by commas |
Input points of interest BED file (*.bed) | 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. |
 | In the Opposite Direction Paired Reads report, paired reads are displayed in blue to indicate the opposite direction. In the Same Direction Paired Reads report, paired reads are displayed in green to indicate the same direction. |
The report is divided into two panes. The Paired Reads View (top) pane is a histogram that shows the distribution of the gap sizes for the read pairs and the position of these pairs in the genome. The Paired Reads Report (bottom) pane is a table that shows information about each read in the pair such as the Read Name, the Read Direction, and so on.
The report is interactive:
Option | Description |
|---|---|
Sort the report results | Double-click any column heading in the report. |
View a position or region in the Alignment viewer | Double-click any value in the report. |
Copy a selected portion of the Paired Reads report to your clipboard | 1. Press and hold the left mouse button, and then drag your cursor over the continuous report cells that you are copying. The selected cells are highlighted in light blue. 2. Right-click anywhere in the selected cells. and on the context menu that opens, select Copy to copy the selected cells to your clipboard. 3. Use standard keyboard commands or menu commands to paste the copied cells into a third-party application. |
Import the region into Pathway Studio and visualize the biological pathway information for the gene | If you have a subscription to Pathway Studio, then you can right-click anywhere in the Paired Reads report, and on the context menu that opens, select View in Pathway Studio. Note: Before you can use the Paired Reads report in conjunction with Pathway Studio, your Pathway Studio access option must be set for the NextGENe Viewer. See Process menu (NextGENe Viewer main menu) in NextGENe Viewer main menu. |
Change the filter settings for the report and dynamically update the report display | 1. On the report menu, click Settings > General Settings. The Filter Settings dialog box opens. 2. Specify the range for which to generate the report, and then click OK to close the dialog box. |
Save the report to a text file | Do either of the following: • On the report menu, click File > Save. • On the report toolbar, click the Save Report icon  .A default name: <project name>_Output_Opposite_Direction_PairedReads or <project name>_Output_Same_Direction_PairedReads and location (the project output folder) are provided for the file, but you can change one or both of these values. |
Specify the information that is displayed in the report |