Output for the Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT primer) workflow

The Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT primer) workflow produces outputs as shown in figure 14.9. The figure shows the results of using the workflow on two samples.

Image fastselect_n6t_workflow_outputs
Figure 14.9: Output from the Perform QIAseq FastSelect RNA Expression and Fusion Calling (N6-T RT primer) workflow when run with two samples.

Two Expression Browsers (Image expression_experiment_16_h_p) tabulate the transcript level expressions of all the samples and the gene level expressions of all the samples.

The Combined_report (Image combine_reports_output_16_h_p) summarizes all the reports generated for all the samples during analysis.

The QC & Reports folder provides detailed reports (Image proteinreport_16_n_p) for individual tools run in the workflow. There is one subfolder per sample. Reports of special interest are:

The Reads folder contains the trimmed reads used in the downstream analysis.

The Gene Expressions and Transcript Expressions folders contain two types of Expression Track (Image rnaseqtrack_16_h_p) - one at the gene level and one at the transcript level. A "filtered" copy of these tracks is also provided. The filtered tracks are limited to genes/transcripts that are annotated as being "protein coding" or "lncRNA". Further details about this track type can be found at https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Expression_tracks.html.

Within the Gene Expressions folder is a PCA plot. This will be empty if there is only a single sample. When there are multiple samples, the clustering in the PCA plot can be used for quality control. For more details on PCA plots see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=PCA_RNA_Seq.html.

The Tracks folders contain the results of fusion calling. There is one subfolder per sample. The results are split into two parts - the "WT" (wildtype) chromosomes, showing reads that align to the reference genome, and the "Fusions" chromosomes showing reads that preferentially align to the fusion products. All the data for the wildtype and fusion chromosomes can be viewed by opening the "Genome Browser View (WT)" (Image trackset_16_n_p) and "Genome Browser View (Fusions)" (Image trackset_16_n_p) respectively. These show the data in the "WT" and "Fusions" folders.

For quality control of fusion calls, see https://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.