The Quantify QIAseq UPX 3' ready-to-use workflow

The Quantify QIAseq UPX 3' ready-to-use workflow can be found here:

        Ready-to-Use Workflows | QIAseq Panel Analysis | Quantify QIAseq UPX 3'

The QIAseq UPX 3' workflow takes demultiplexed samples (see Demultiplex QIAseq UPX 3' reads) to be run in batch mode as highlighted in figure 6.2.

Image upxselectreads
Figure 6.2: Human or Mouse QIAseq UPX 3' ready-to-use workflows only require demultiplexed reads.

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 report expression across the whole genome, which allows the user 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.