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

To export a BAM file relative to an ROI BED file

To export a BAM file for the alignment results for the regions defined only in the BED file, select ROI BAM as an export option.

1. On the Export dropdown list, select ROI BAM.

A blank Settings field opens next to the ROI BAM option.

2. Next to the blank Settings field, click Set and then browse to and select a saved BED (*.bed) file.

3. Repeat Step 1 and Step 2 until you have added all the needed BED files.

4. If Export ROI 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 the project output to a BAM file.

• To export the output to Geneticist Assistant.