To specify the information that is displayed in the Paired Reads report
 | The following procedure describes how to set up an entirely new Paired Reads report. Optionally, you can click Load on the Paired Report Settings dialog bxo to browse to and select a Settings file (.ini file) to generate the report based on the saved settings in the file. |
1. On the report menu, click Settings > Display Settings.
The Paired Report Settings dialog box opens.
2. Do any of the following as needed:
• To hide show only the Paired Reads Report (bottom) pane, clear the Histogram option. Conversely, to display the Paired Reads View (top) pane again, click histogram.
• To show only the Paired Reads View (top) pane, clear the Table option. Conversely, to display the Paired Reads Report (bottom) pane again, click Table.
 | Both of these options are also available from the Show Paired Reads View  icon and Show Paired Reads Report  icon that are displayed on the report toolbar. |
• To include a column in the Showed Paired Reads Report display, select the column. Conversely, to hide a column from the display, clear the column option.
Column | Description |
|---|---|
Read Dir | The direction (Forward or Reverse) for the read. |
5’ pos | The starting position for the 5’ end of the read. |
3’ pos | The ending position for the 3’ end of the read. |
5’ Gap distance | The distance in bp between the starting 5’ position for the first read and the ending 5’ position for the second read. |
Contig | The contig where the read is aligned. |
Chr | The chromosome where the read is aligned. |
5’ chr pos | The chromosome position for the 5’ end of the read. |
3’ chr pos | The chromosome position for the 3’ end of the read. |
Gene | The gene where the read is aligned. |
Exon | The exon where the read is aligned. Includes both coding and non-coding exons. |
CDS | The coding exon where the read is aligned. |
| | When you select an option, two columns are displayed in the report, one for each read in the pair. |
| | Optionally, before the next step, you can click Save on the Paired Report Settings dialog box to save the settings for the report in a Settings file (.ini file), which can be used to generate the Paired Reads report for another project based on the settings in the file. |
3. Click OK.
The Paired Report Settings dialog box closes and the report display is dynamically updated.