Running tools and workflows

When CLC Single Cell Analysis Module is installed, the toolbox is populated with Single Cell Analysis specific tools and workflows. These include single cell related importers described in Data import, and single cell related exporters described in Data export. In addition, the Single Cell Analysis folder will appear in the Toolbox, and the Single Cell Workflows folder will appear in the Template Workflows section. To launch a tool or workflow either double-click it in the toolbox or use the quick launch button (figure 3.1). 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.

Image launch
Figure 3.1: The Launch button is situated in the top left corner of the workbench.

Running tools

All tools require an input. In many cases this will be an imported Expression Matrix (Image expression_matrix_track_16_n_p) / (Image expr_matrix_spliced_unspliced_16_n_p), Peak Count Matrix (Image peak_count_matrix_16_n_p), or Cell Clonotypes (Image cell_tcr_clonotypes_16_n_p) / (Image cell_bcr_clonotypes_16_n_p), or, when starting from FASTQ, imported reads. See Data import for how to import files in formats specific to single cell data.

Tools will only run correctly when meaningful input and parameters are provided. If a warning is shown, read it carefully as it will in most cases guide you to the problem.

Select the input based on the description provided in the tool. Although most tools will only allow selection of the correct data type as input, it may still be possible to provide input that does not conform to the tool's expectations. If this happens, the tool will give a warning or gray-out options that cannot be used. The default settings for each tool are suitable for most use cases, but some settings require knowledge of sample preparation or sequencing technology. Most problems arise from inappropriate settings. If a tool produces a report, make sure to inspect it, as it may provide quality control or guidance for how to change settings.

For a full description of running tools, handling results and batch options see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_tools_handling_results_batching.html.

Running workflows

CLC Single Cell Analysis Module provides template workflows for analyzing scRNA-Seq, scATAC-Seq, and scV(D)J-Seq data in multiple steps. Input can either be selected from the navigation area or imported using Select files for import. Make sure to select the correct import type.

Follow the instructions in the wizard steps and save the data by specifying a location in the navigation area. Read more about the provided workflows and how to select proper parameters in Single cell template workflows from reads and Single cell template workflows from imported data.

For a full description of how to launch workflows and use metadata see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Launching_workflows_individually_in_batches.html.