Quantify QIAseq UPX 3'

The Quantify QIAseq UPX 3' template workflow can be found here:

        Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | QIAseq Sample Analysis (Image qiaseqrna_folder_closed_16_n_p) | Analyze QIAseq Samples (Image qiaseq_panel_guide_16_h_p)

Where it is available on the UPX 3' RNA tab in the guide.

The QIAseq UPX 3' workflow takes demultiplexed samples (see Demultiplex QIAseq UPX 3' reads) to be run in batch mode as highlighted in figure 15.41.

Image upxselectreads
Figure 15.41: 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.

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 (Image biomedical_twf_folder_open_16_n_p) | QIAseq Sample Analysis (Image qiaseqrna_folder_closed_16_n_p) | QIAseq RNA Workflows (Image qiaseq_workflows_folder_closed_16_n_p) | Quantify QIAseq UPX 3' (Image quantify_qiaseq_upx_16_n_p)

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=Creating_editing_workflows.html.



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