Output from the Quantify QIAseq RNA Expression workflow

The Quantify QIAseq RNA Expression template workflow produces expression tracks (Image rnaseqtrack_16_h_p) for each sample together with a combined report containing QC metrics (Image combinedreport_16_n_p). These reports can be used as input to Combine Reports to make a summary report for many samples. A Workflow Result Metadata table keeping track of all generated output and a log file will also be generated as default outputs. See (figure 15.39).

Image quantify_qiaseq_rna_output
Figure 15.39: The output files of the Quantify QIAseq RNA Expression workflow.

Expression tracks are displayed as tables listing genes included in the panel and several measures of their expression levels.

Expression tracks can be further analyzed using statistical tools from the RNA-Seq Analysis folder of the workbench, such as PCA for RNA-Seq and Create Heat Map for RNA-Seq.

QC metrics can be found in the combined report. They indicate how many reads were ignored and the reason they were not included in a UMI read. The "Accepted reads" column contains the number of reads that passed the filtering carried out by Quantify QIAseq RNA, see Quantify QIAseq RNA.

When you are designing a customized panel online, you will see that there is an option to add a set of 6 "GDC controls". These values are your negative controls of genomic DNA. You can also see these in the target regions where they have names like "GDC_CONTROL_06". The number of control targets with more than 10 UMI reads are listed in the "Expressed GDC controls" table cell. This cell will be colored pink and a warning will be shown if any controls are expressed.

Why does the workflow not produce a read mapping?

The very short target regions in a QIAseq Targeted RNA Panel are not suited to downstream analyses that require a read mapping, such as variant calling. If a read mapping is desired, for example to investigate suspected off-target effects, we recommend using the Map Reads to Reference tool.