Folders
The following output folders are generated during an analysis session.
| • | Alignment - BAM with aligned and noncollapsed sequencing reads |
| • | CollapsedReads - BAM with aligned and collapsed sequencing reads, and intermediate metrics |
| • | Stitched – Intermediate BAM and metrics files |
| • | Logs – Log files for individual analysis steps including stdout and stderr |
| • | Report – csv formatted report with metrics, software versions, run time, and analysis information |