Output from the Detect QIAseq RNAscan Fusions workflow

The Detect QIAseq RNAscan Fusions workflow's main outputs are two Genome Browser Views.

Genome Browser View (WT) displays the following tracks:

Genome Browser View (Fusions) displays the following tracks:

In addition, the workflow outputs a series of folders: Tracks", "Read Mappings" and "Fusions References" contains the tracks included in the Genome Browser both for Wild Type and Fusions; "QC and Reports" contain the following reports:

Note about interpreting the QC for RNAscan Panels Report The relationship between input, amplification and therefore number of reads per UMI with the original coverage is complex. For example, a "good" original coverage can be deceiving, if the user has amplified many times the original molecule: in that case, the information added to the experiment is close to null.

The easiest way to review the results is to open the Genome Browser Views.

The read mapping track displays the mapping of UMI reads to the transcript sequences. It contains only reads that provide conclusive evidence for or against fusion (figure 4.4).

Image rnascanoutput
Figure 4.4: An example of fusion in a Genome Browser View.

Double-click on the fusion track name (to the right of the Genome Browser View) while pressing the Ctrl button. The fusion track will open as a table in split view, below the Genome Browser View. Clicking on a fusion event in the table will zoom in to its location in the UMI read mapping, allowing you to review the UMI reads supporting the detected fusion. Note that each fusion event is represented by two lines in the table sharing the same Fusion number. Each line corresponds to a fusion breakpoint.

Note about exporting output files in SAM/BAM format Exporting UMI reads as BAM files will show UMI described as Unique_Molecular_Index=[number1]_count=[number2], where number1 is a UMI ID (just a unique UMI group number), and number2 is the number of reads that are in that UMI group.

The fusion table contains the following information: