To use the Batch CNV tool
1. On the Comparisons menu, select Batch CNV Tool.
The Batch CNV Tool dialog box opens.
2. Do one of the following:
• To select the folder that contains all the sequence alignment projects (*.pjt) that are to be compared, click Batch Add, and then browse to and select the folder.
 | You can select a top-level folder in a directory, and NextGENe scans not only the top-level folder for *.pjt files, but also all the associated sub-folders. |
• To add one sequence alignment project (*.pjt) at a time, click Add, and then browse and select a project. Repeat this step as needed to select all the required projects.
3. Click Set, and then browse to and select the BED file that is to be used to define the regions for the projects.
4. Optionally, to limit the report results do the following:
a. Create a text file that lists the descriptions for selected regions of this file. (Each description must be its own line entry.)
b. Click Set, and then browse so and select this text file.
Although all calculations are carried out on the whole BED file, only those regions of the uploaded BED file that have descriptions that match those contained in the text file are included in the Batch CNV report.
5. Click OK.
The Batch CNV report is generated. Each report column represents a different sequence alignment project, and each report row represents a different region in the BED file. The default range for the average normalized coverage is 0.8 to 1.2. The closer that the normalized average coverage is to one for a given project/region combination, the greater the likelihood that the region does not contain a CNV relative to all the other projects that were loaded. The region names are taken from the 4th column of the BED file that used to define the regions for the projects.
The Batch CNV report is interactive:
• To load different projects and/or BED file, on the report toolbar, click the Load Projects icon 
to open the Batch CNV Tool dialog box, and make the appropriate changes.
to open the Batch CNV Tool dialog box, and make the appropriate changes.• To save the report to a text file, on the report toolbar, click the Save Report icon 
. A default name and location are provided for the file, but you can change both of these values.
. A default name and location are provided for the file, but you can change both of these values.• To generate a graphical display of the data, on the report toolbar, click the Batch CNV Graphs icon 
. See Batch CNV graphs.
. See Batch CNV graphs.