The Detect QIAseq RNAscan Fusions ready-to-use workflow

The Detect QIAseq RNAscan Fusions ready-to-use workflow can be found in the Toolbox here:

        Ready-to-Use Workflows | QIAseq Panel Analysis | Detect QIAseq RNAscan Fusions

Double-click on the Detect QIAseq RNAscan Fusions ready-to-use workflow to run the analysis.

If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.

The following dialog helps you set up the relevant Reference Data Set. If you have not downloaded the Reference Data Set yet, the dialog will suggest the relevant data set and offer the opportunity to download it using the Download to Workbench (figure 4.1).

Image selectrdsrnascan
Figure 4.1: The relevant Reference Data Set is highlighted; in the text to the right, the types of reference needed by the workflow are listed. There is also an indication of how many data set can be used with the workflow. In this case, the other data sets would only be visible when opening the "QIAGEN Previous" or "QIAGEN Tutorial" folder.

Note that if you wish to Cancel or Resume the Download, you can close the ready to use workflow and open the Reference Data Manager where the Cancel, Pause and Resume buttons are available.

If the Reference Data Set was previously downloaded, the option "Skip data set selection and use defaults" is available and will ensure the relevant data set is used. You can always check the "Select data set" option to be able to specify another Reference Data Set than the one suggested.

In the Select reads dialog, specify the sequencing reads that should be analyzed (figure 4.2).

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Figure 4.2: Select the sequencing reads by double-clicking on the file name or by clicking once on the file name and then on the arrow pointing to the right hand side.

In the Select primers dialog, chooses the file that corresponds to the panel that was used to generate the reads (figure 4.3). You can find it in the CLC_References folder after you have downloaded the QIAseq RNAscan Panels hg38 Reference Data Set. The easiest way to access that file is to look for it using the Reference Data tab.

Image selectprimersrnascan
Figure 4.3: Select the primer track for the relevant panel.

In the Detect Fusion Genes dialog, it is possible to change the Promiscuity threshold, i.e., the minimum number of different fusion partners needed to deem a gene promisucous. You can also check the Detect exon skipping option to consider same-gene fusions, i.e., exon-skipping fusions. Note however that same-gene fusions where the 5' breakpoint is downstream of the 3' breakpoint will not be considered. Also excluded are exon-skipping fusions that were already annotated on other transcripts from the mrNA track selected.

Finally, in the last wizard step, choose to Save the results of the workflow and specify a location in the Navigation Area before clicking Finish.