To export the project output to a BAM file

NextGENe Online Help : The NextGENe AutoRun Tool : Batch Processing of Multiple Projects : To create a new job file in the NextGENe AutoRun tool : To export the project output to a BAM file

Select Export BAM to automatically generate a BAM file for the alignment results for the project. If you export NextGENe sequence alignment project files to a BAM format, then the standard index file, index.bai, that other alignment viewers require is also exported. If you do not select this post-processing option, you always have the option of exporting the project output to a BAM format from the File menu on the NextGENe viewer. (See NextGENe Viewer main menu.) If Export BAM is the only needed processing option, then return to one of the following as appropriate:

• Step 12 of To create a new job file in the NextGENe AutoRun tool.

• Step 5 of To create a single post-processing Settings file.

• Step 7 of To create a new job from an existing AutoRun template.

• Step 9 of To create a NextGENe AutoRun template.

• Step 5 of To modify a NextGENe AutoRun template.

• Step 6 of To modify a NextGENe AutoRun pre-built template.

Otherwise, continue specifying any other needed post-processing options. See:

• To select the Mutation Report as a post-processing option.

• To select a report other than the Mutation report as a post-processing option.

• To export aligned sequences as a post-processing option.

• To export a BAM file relative to an ROI BED file.

• To export the output to Geneticist Assistant.