The Quantify QIAseq UPX 3' template workflow can be found here:
Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | Analyze QIAseq Samples ()
Where it is available on the UPX 3' RNA tab in the guide.
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.
Be aware that 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.
Note: If there is a need to adjust any of the parameters in the tools used in the workflow the Quantify QIAseq UPX 3' template workflow can be found here for configuration:
Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | QIAseq Analysis Workflows () | Quantify QIAseq UPX 3' ()
Right click and open a copy of the workflow for adjusting the needed parameters for each tool. More information about how to configure a workflow can be found here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Editing_existing_workflows.html.