Analyze QIAseq RNAscan
The Analyze QIAseq RNAscan template workflow can be used for analyzing data produced with the QIAseq Targeted RNAscan Panels.
The workflow includes all necessary steps for processing and analyzing the reads:
- Various statistics summarizing and visualizing the input reads are produced using QC for Sequencing Reads.
- UMIs are removed using Remove and Annotate with Unique Molecular Index.
- Reads are trimmed using Trim Reads.
- UMI reads are created using Create UMI Reads from Reads.
- Expression is quantified using RNA-Seq Analysis.
- Fusions are detected using Detect and Refine Fusion Genes.
- A QC report and primer coverage statistics for the mapped reads are created using QC for RNAscan Panels.
- A summary report is created using Create Sample Report.
- A report is optionally prepared for uploading to QCI Interpret using Prepare QCI Interpret Upload.
Launching the workflow
To run this workflow, go to:
Workflows | Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq RNA Workflows (
) | Analyze QIAseq RNAscan (
)
See Launching workflows individually and in batches for general information.
Options can be configured in the following wizard steps:
- Choose where to run. 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.
- Specify workflow path. The following path can be configured:
- Prepare for QCI Interpret. Prepare a report that can later be uploaded to QCI Interpret or QCI Interpret Translational.
- Select Reads. Select the input reads. When analyzing more than one sample at a time, check Batch in the lower left corner of the dialog.
- Specify reference data handling. Select the QIAseq RNAscan Panels hg38 Reference Data Set, see Reference data management for details.
- Configure batching, if running the workflow in batch mode. Define the batch units.
- Batch overview, if running the workflow in batch mode. Verify that the batching is as intended.
- Target primers. Choose the relevant primers from the drop down list.
- Remove and Annotate with Unique Molecular Index. Select "Paired end reads (index on read 2)" for Illumina data or "Single end reads" for Ion Torrent data.
- Create UMI Reads from Reads. Select "Paired end reads" for Illumina data or "Single end reads" for Ion Torrent data.
- Detect and Refine Fusion Genes. Configure the following options as needed:
- Detect exon skippings
- Detect novel exon boundaries
- Detect novel exon boundaries in both genes
- Gene filter action
- Genes for filtering (tracks)
- Fusion filter action
- Fusions for filtering (tables)
For details about the elements used by default in 'Genes for filtering (tracks)' and 'Fusions for filtering (tables)', see Exclude lists.
For general details about fusion detection, see Detect and Refine Fusion Genes.
- Create Sample Report. Select relevant summary items and configure thresholds for quality control. These are included in the quality control section of the sample report. The default values are appropriate for most data sets, but may need to be adjusted.
- Prepare QCI Interpret Upload, if preparing a QCI Interpret report. Specify sample name, subject ID, and project.
- Result handling. Choose if a workflow result metadata and/or log should be saved.
- Save location for new elements. Choose where to save the data, and press Finish to start the analysis.
Launching using the QIAseq Panel Analysis Assistant
The workflow is also available in the QIAseq Panel Analysis Assistant under Targeted RNAscan.
Subsections