SAM/BAM Output
When you export the NextGENe sequence alignment project files for the project that is currently opened in the NextGENe viewer to a SAM or BAM format, the standard index file, index.bai, that other alignment viewers require is also exported.
1. Click File > Export > SAM/BAM Output.
The SAM/BAM Output dialog box opens.
2. Select the appropriate export format and then optionally, click Set to browse to and select the location for the exported file.
 | The default location is the project output folder. |
3. Optionally, to indicate which regions to include/exclude for the BAM or SAM file, select Filter by ROI, and then to:
• Indicate the regions that are to be included in the BAM or SAM file, click Add for the Inclusion pane, and then select the appropriate BED file.
• Indicate the regions that are to be excluded from the BAM or SAM file, click Add for the Exclusion pane, and then select the appropriate BED file.
4. Optionally, click Select Chromosome.
The Select Chromosome dialog box opens.
5. Specify the chromosomes to include in/exclude from the export file (by default, all chromosomes are included), and then click OK. You can:
• Select/deselect an individual chromosome.
• Select/deselect All chromosomes in a single step.
• Select/deselect all Unlocalized (sequences) in a single step, which are contigs that are known to be part of a particular chromosome, but the locations within the chromosome are not known.
• Select/deselect all Unplaced (sequences) in a single step, which are contigs for which the specific locations, including the chromosome, are not known.
6. Click OK.
The Select Chromosomes dialog box closes. You return to the SAM/BAM Output dialog box.
7. Click OK.
The dialog box closes. The export is carried out.