To specify the post-processing options for a Sequence Alignment project
Optionally, you can specify post-processing options for a sequence alignment project.
• Report post-processing options—If you specify report post-processing options, then selected reports, including the Summary report, are generated automatically and saved for the project after project analysis is completed. Each report is generated and saved based on the settings that were specified in a saved Settings file (.ini file) for the report. You can generate and save multiple versions of different reports, or multiple versions of the same report as long as each report version uses a different Settings file. To specify post-processing options for the first time, you must have previously saved a Settings file for at least one of the following reports:
• Mutation report (The general report settings and/or the variation tracks settings). See Sequence Alignment Project Mutation Report Settings.
• Distribution report. See Distribution Report.
• Coverage Curve report. See Coverage Curve Report.
• Expression report. See Expression Report.
• Structural Variation report. See Structural Variation Report.
• HLA report. See HLA project report.
 | The HLA report is available as a post-processing option only if HLA is selected as the application type. See HLA Analysis Project in the NextGENe Sequence Alignment Tool. |
• Transcript report. See Transcript report.
| | The Transcript report is available as a post-processing option only if Transcriptome with Alternative splicing is selected as the application type. See Transcriptome Alignment Project with Alternative Splicing in the NextGENe Sequence Alignment Tool. |
• Summary report. See Summary Report.
| | Save Summary Report is available only after you select at least one other post-processing report and its Settings file. The information that is contained in the Summary report is relative to the post-processing reports that you select for the project. |
• Export post-processing options:
• Export Sequence – If you specify export sequence post-processing options, then a .fasta file that contains all the reads that aligned to a specific region in the reference sequence is automatically generated after project analysis is completed. The sequence is generated and saved based on the settings that were specified in a saved Settings file (.ini file) for the sequence. To specify post-processing options for the first time, you must have previously saved a Settings file for the sequence using the Export Sequences tool. See Export Sequences tool.
• Export ROI BAM – If you specify ROI BAM as a post-processing option, then instead of the entire BAM file being exported, a BAM file for alignments that fall only within the ROIs is exported.
You can also export the project output to just a BAM file, and you can export the project output (BAM and VCF files) to Geneticist Assistant.
1. Click Post Processing.
The Post Processing page opens.
2. Select any of the post-processing options as needed. See: