Perform TSO500 RNA Analysis

The Perform TSO500 RNA Analysis (Illumina) workflow includes all necessary steps for processing paired-end reads from TSO500 RNA samples, such as sample QC, adapter trimming, mapping resulting in gene expression counts and fusion gene identification.

The workflow can be found in the Toolbox at:

        Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | TSO Panel Analysis (Image tso500_folder_closed_16_n_p) | Perform TSO500 RNA Analysis (Illumina) (Image tso500_fusion_gene_detection_16_n_p)

If you are connected to a CLC Server via the CLC 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.

In the next step, select the RNA sequencing reads to analyze. The input can be sequence lists containing paired-end reads selected from the Navigation Area, or samples can be imported using the "Select files for import" option, where files containing paired-end read data can be selected from disk. If choosing the "Select files for import" option, the "Paired reads" option needs to be enabled.

If you would like to analyze more than one sample in one workflow run, check the "Batch" box in the lower left corner of the dialog. When analyzing multiple imported samples, metadata needs to be provided. Further information can be found at

After selecting reference data as described below you can configure the batch unit and see the batch overview. When using metadata, selecting an Excel file that describes the data will often be the most convenient method. Providing metadata directly from an Excel file is the only option available when input data is imported as part of the workflow run.

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. The dialog for selection of reference data is shown in figure 17.2.

Image tso500_rna_rds
Figure 17.4: The relevant Reference Data Set is highlighted. The text to the right lists the types of references needed by the workflow.

Note that if you wish to Cancel or Resume the Download, you can close the template 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 next step, you can adjust the parameters for specifying the fusion gene detection (figure 17.5).

The Configurable Parameters for Detect and Refine Fusion Genes are:

Image tso500fusiongenewizard
Figure 17.5: Adjustable parameters for the Detect and Refine Fusion Genes wizard step. Options include detection of exon skipping and fusions with novel exon boundaries.

Finally, choose where to save the results.