Output from the Perform QIAseq Multimodal RNA Library Kit Analysis workflows
The following outputs are generated:
- Gene expression: A track with gene expression annotations, including counts and expression values for each gene. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_result_handling.html for details.
The track produced by the Perform QIAseq Hybrid Capture RNA Analysis (Illumina) (beta) workflow contains only the genes targeted by the QIAseq xHYB CGP RNA Panel.
- Genome Browser View (
): A collection of output tracks, allowing multiple data types at the same genomic position to be viewed simultaneously. Note that not all output tracks are necessarily in the browser. Tracks can be added and removed from the browser as described in https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Track_lists.html.
If running fusion detection, two browsers are generated, one for wild type (WT) and one for the artificial fusion chromosomes.
- PASS fusion genes (WT) (
), if running fusion detection: The breakpoints on the reference genome of detected fusions that have passed all relevant filters. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Output_from_Detect_Refine_Fusion_Genes_tool.html for details.
- Sample report (
): A report containing essential information from all reports produced by the workflow. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report_output.html for details.
- QC & Reports folder:
- Fusion report (
): Summarizes the identified fusions. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Output_from_Detect_Refine_Fusion_Genes_tool.html for details.
- QC report (): Summarizes and visualizes various statistics of the input reads. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Sequencing_Reads.html for details.
- Remove and annotate UMI report (): Summarizes the identified UMIs. See Remove and Annotate with Unique Molecular Index for details.
- RNA-Seq report (): Summarizes various mapping statistics and biotypes distributions. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_report.html for details.
- Trim adapters, Trim homopolymers, and Trim on quality reports (): Summarize the performed trimming. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_output.html for details. The order of these three trimming steps can be seen in the sample report.
- UMI reads report (): Summarizes the identified UMI groups. See Create UMI Reads from Reads for details.
- Fusion report (
- Tracks folder:
- Read mapping (
): The reads mapped to the reference genome. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_result_handling.html for details.
- Gene expression unfiltered (
), if running the Perform QIAseq Hybrid Capture RNA Analysis (Illumina) (beta) workflow: An unfiltered track with gene expression annotations, including counts and expression values for each gene. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_result_handling.html for details.
If running fusion detection, additional output tracks are organized in two subfolders:
- WT:
- Fusion genes (WT) (): The breakpoints on the reference genome of all detected fusions.
- Read mapping refined (WT) (): The reads that mapped best to the reference genome. See also Read mapping (fusions) below.
- Unaligned ends (WT) (): The unaligned ends mapped to the reference genome.
- Fusion genes (WT) (
- Fusions:
- Reference sequence (fusions) (
) , Genes (fusions) (), mRNA (fusions) (), and CDS (fusions) (): The reference sequence, gene regions, mRNA transcripts, and CDS regions corresponding to the detected fusions on the artificial fusion chromosomes.
- Fusion genes (fusions) (): The breakpoints on the artificial fusion chromosomes of all detected fusions.
- Read mapping (fusions) (): The reads that mapped best to the artificial fusion chromosomes.
- Reference sequence (fusions) (
- Read mapping (