Output from the Quantify QIAseq RNA Expression workflow
The Quantify QIAseq RNA Expression ready-to-use workflow produces expression tracks (
) for each sample analyzed.
Expression tracks are displayed as tables listing genes included in the panel and several measures of their expression levels.
- Expression value The number of distinct UMIs seen for this gene.
- TPM (Transcripts per Million) The number of transcripts per million that come from this gene. This is computed as the relative abundance per million
.
- RPKM (Reads Per Kilobase per Million reads) There is no good definition of RPKM for targeted amplicon data. We therefore define RPKM to be equal to TPM, which preserves the expected property that RPKM is proportional to TPM.
- Total gene reads The number of distinct UMIs seen for this gene.
- Read counts The total number of reads mapping to this gene. Several reads may have the same UMI.
- UMI counts The number of distinct UMIs seen for this gene.
- Mean reads per UMI The mean number of reads for each UMI seen for this target.
Expression tracks 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.
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.