The Quantify QIAseq UPX 3' template workflow
The Quantify QIAseq UPX 3' template workflow can be found here:
Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | Quantify QIAseq UPX 3' (
)
These workflows can also be launched from the Analyze QIAseq Samples guide, which is described in The Analyze QIAseq Samples guide. They are available in the drop down menus under each panel analysis listed on the UPX 3'RNA tab.
The QIAseq UPX 3' workflow takes demultiplexed samples (see Demultiplex QIAseq UPX 3' reads) to be run in batch mode as highlighted in figure 11.2.
Figure 11.2: Human or Mouse QIAseq UPX 3' template 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 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.
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