Output from the Perform QIAseq Multimodal RNA Lib Kit Analysis workflows
The following outputs are generated:
- Genome browser view (
): A collection of output tracks, allowing multiple data types at the same genomic position to be viewed simultaneously. These tracks are located in the Tracks folder and are described below. Note that not all output tracks are 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 output, one for wild type (WT) and one for the fusion chromosomes.
- 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.html for details.
- QC & Reports folder:
- QC report (
): Summarizes and visualizes various statistics of the input RNA 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.
- Trim adapters, Trim homopolymers, and Trim 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.
- 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.
- Fusion report (), if running fusion detection: 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 (
- Tracks folder:
If running fusion detection, the tracks outputs are organized in two subfolders: WT and Fusions.
The following tracks are saved by both workflows and output by RNA-Seq Analysis. If running fusion detection, they are located in the WT subfolder. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_result_handling.html for more details about the outputs.
- Gene expression and Transcript expression: Summarize expression at the gene and transcript level.
- Gene expression filtered and Transcript expression filtered: Summarize expression at the gene and transcript level for genes/transcripts with protein_coding and lncRNA biotypes.
- Read mapping: The reads mapped to the reference genome.
The following tracks are only saved when running fusion detection. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Output_from_Detect_Refine_Fusion_Genes_tool.html for more details about the outputs.
- WT/Fusion genes unaligned ends (WT): The unaligned ends mapped to the reference genome.
- WT/Read mapping refined (WT): The reads that mapped best to the reference genome. See also Fusions/Read mapping (fusions) below.
- WT/Fusion genes (WT): The breakpoints on the reference genome of all detected fusions.
- Fusions/Reference sequence (fusions), Genes (fusions), mRNA (fusions), and CDS (fusions): The reference sequence, gene regions, CDS regions, and mRNA transcripts corresponding to the detected fusions on the artificial fusion chromosomes.
- Fusions/Read mapping (fusions): The reads that mapped best to the artificial fusion chromosomes.
- Fusions/Fusion genes (fusions): The breakpoints on the artificial fusion chromosomes of all detected fusions.
- VCF Exportable Tracks folder, if running fusion detection.
The output that can be exported using the VCF exporter.
- PASS fusion genes (WT): The breakpoints on the artificial fusion chromosomes of detected fusions that have passed all relevant filters.