The Quantify QIAseq UPX 3' ready-to-use workflow can be found here:
Ready-to-Use Workflows | QIAseq Panel Analysis () | Quantify QIAseq UPX 3' ()
These workflows can also be launched from the Analyze QIAseq Panels guide, which is described in The Analyze QIAseq Panels guide.They are available in the drop down menus under each panel analysis listed on the UPX 3'RNA tab.
Then either a human or mouse specific workflow is run using either QIAseq UPX Panels hg38 or QIAseq UPX Panels Mouse. Note that it is not possible to make custom panels - instead the workflow always reports expression across the whole genome, which allows you to see when reads map off-target.
Note: The Quantify QIAseq UPX 3' workflow is configured to expect reads that are strand specific. This is because the reaction design ensures that reads from 3' fragments will appear forward-stranded (read 1 mapping sense to the transcript). It is not unusual for 5-10% of reads to be dropped in the workflow for having an unexpected strandedness.