Output from the Perform QIAseq RNA Fusion XP Analysis workflow

The Perform QIAseq RNA Fusion XP Analysis workflow's main outputs (figure 14.7) are two genome browser views, a gene expression track, a fusion report and a fusion track (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Output_from_Detect_Refine_Fusion_Genes_tool.html), and a sample report that contains summary information from reports output by multiple tools in the workflow.

Image xpoutputfolders
Figure 14.7: Outputs of the Perform QIAseq RNA Fusion XP Analysis workflow for an input called "M1750-850-4-7_S1_L001_R1_001 (paired)"

Genome Browser View (WT) displays the following tracks:

Genome Browser View (Fusions) displays the following tracks:

Many of the track outputs included in the Genome Browser Views are placed in two folders: "Tracks | WT" and "Tracks | Fusions".

Detailed reports that are summarized in the sample report are placed in a folder called "QC & Reports". These include:

The VCF Exportable Tracks folder contains outputs that can be exported together as a single VCF file using the VCF exporter. This folder contains a Variant Track of RNA variants passing filters, and a track of fusions.

A second Variant Track of RNA unfiltered variants is found in the "Tracks | WT" folder. This is provided so that you can also review why a variant that was expected in the output has been filtered out of the RNA variants passing filters track.

The difference between the RNA unfiltered variant track and the RNA variants passing filters track depends on the following options available in the filtering steps:

For quality control of fusion calls, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Interpretation_fusion_results.html. We particularly recommend carrying out manual quality control checks on results that include fusions with novel exon boundaries.