The Detect QIAseq RNAscan Fusions ready-to-use workflow

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

        Ready-to-Use Workflows | QIAseq Panel Analysis (Image qiaseqrna_folder_closed_16_n_p) | QIAseq Analysis Workflows (Image qiaseq_workflows_folder_closed_16_n_p) | Detect QIAseq RNAscan Fusions (Image fusion_gene_detection_16_h_p)

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 button. (figure 7.1).

Image selectrdsrnascan
Figure 7.1: 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 sets 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 "Use the default reference data" is available and will ensure the relevant data set is used. You can always check the "Select a reference set to use" option to be able to specify another Reference Data Set than the one suggested.

In the Select reads dialog, specify the sequencing reads to analyze (figure 7.2).

Image selectreadsgfd
Figure 7.2: 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, choose the file corresponding to the panel used to generate the reads (figure 7.3). 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 under the Reference Data tab.

Image selectprimersrnascan
Figure 7.3: Select the primer track for the relevant panel.

In the Detect and Refine Fusion Genes dialog, it is possible to change the Promiscuity threshold, i.e., the maximum number of different fusion partners reported for a gene. You can also check for exon skippings by enabling the Detect exon skippings option, as well as check for fusions with novel exon boundaries by enabeling the Detect fusions with novel exon boundaries option.

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