Distribution Report
By default, the Distribution report shows the coverage distribution across the whole reference sequence.If you are carrying out targeted sequencing then to view the coverage distribution for specific regions, use the option to load a BED file.
 | To load a BED file, on the Distribution report menu, click File > Load BED file. |
The Distribution report provides four different charts that display coverage information for the alignment project. All four charts display information for both forward and reverse reads, with the forward reads represented in blue and the reverse reads represented in red. The reverse coverage is stacked on top of the forward coverage. From top to bottom, the charts display the following unique information:
• For projects that include condensation, the Original Coverage chart displays the coverage distribution for the original reds that were used for condensation. For projects that did not include condensation, the chart is not displayed.
• The Directional Coverage chart displays the coverage of the reads across the reference sequence.
• The Sequence Starting Location chart displays the distribution of the sequence starting points.
• The Read Length Distribution chart shows the distribution by read lengths.
The report is interactive:
• To change the charts that are displayed and/or to change the position information, on the report menu, click View, and then on the View menu, clear the selections for the charts/position information that are not to be displayed. By default, all charts are displayed, and the position information is shown as Chr (chromosome) positions. If you clear Chr Positions, then reference position is displayed instead.
| | The Original Coverage option is displayed on the View menu only if you are viewing condensed data. |
• To save the exact coverage information for any location or region, on the report menu, click File > Save Coverage to open the Save Coverage Settings dialog box, and on the General tab, specify how to save the coverage information. Optionally, you can click Load Settings and browse to and select a Settings file (.ini file) to save the coverage information based on the saved settings in the file.
Setting | Description |
|---|---|
• Condensed • Original | Available only if the project included condensation. Indicate to save coverage for either condensed reads or original reads. |
Specify the coverage region for which you want to save the coverage settings. You can select one of the following: | |
• Input region manually | • Input the region manually. (You must specify the starting position and the ending position.) |
• 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: • Specific reference locations (position number or a range of positions (start position number - end position number)) separated by commas • A list of reference gene names separated by commas |
• Input region 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 |
• Save coverage for ROI | • Save the coverage information based on Regions of Interest as defined in the GenBank reference file. Note: For information about creating Regions of Interest in a GenBank reference file, see Advanced GBK Editor tool. |
• Save coverage for entire reference range | • If you select this option, then coverage is saved for the entire region, which means that you do not need to manually specify a range. |
Ignore the uncovered regions | Select this option to exclude uncovered regions from the Save Coverage Settings report. |
Step | You must set the Step value, which is the increment (for example, >1) at which the coverage is to be measured. |
• Average • Sum | Report the coverage as either the average value for a region or the sum total of all covered bases across the region. Note: If Step =1, then because the coverage for every base is reported, there is no difference between the two options. |
• You can open the Summary Report tab, and then do one or both of the following:
• Specify an alternate name for the Distribution report when it is displayed in the Summary report.
• Clear the options for the sections of the Distribution report that are not to be included in the Summary report.
| | Display original coverage is available only if you are viewing condensed data. |