Output from the Quantify QIAseq UPX 3' workflow

The Quantify QIAseq UPX 3' workflow generates the following outputs:

Note that the Quantify QIAseq UPX 3' workflow discards reads that map to multiple genomic locations. This can lead to genes with homologs or containing repetitive regions being reported as having low or no expression. In order to estimate expressions including multi-mapping reads, open a copy of the workflow and untick the option "Exclude ambiguously mapped reads" in the Calculate Unique Molecular Index Groups tool.

Notes about the RNA-Seq report:

Use Gene Expression tracks to perform Differential Expression. If the analysis is set up as a single-cell experiment, a clustering of the data could provide more insights. All the tools available for downstream analyses can be found in the RNA-seq Analysis folder of the Toolbox.