Output from the Perform QIAseq UPXome RNA Analysis workflow
The following outputs are generated:
- Combined report (
): A report containing essential information from all reports produced by the workflow for all samples. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Combine_Reports_output.html for details.
- Gene expression browser (
): A browser for inspecting feature expressions, annotations, and statistics for all samples. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=_expression_browser.html for details.
If running fusion detection, two browsers are generated, one for gene expressions from all reads and one for gene expressions from the N6-T RT primer reads only.
- 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 and one for the fusion chromosomes.
- PCA plot (
): A Principal Component Analysis (PCA) plot. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=PCA_RNA_Seq.html for details.
If using both ODT-T RT and N6-T RT primers, two plots are generated, one for gene expressions from all reads and one for gene expressions from N6-T RT primer reads only.
- QC & Reports folder:
- Demultiplex report (
): Summarizes the number of reads found for each barcode, i.e. for each sample. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Output_from_Demultiplex_Reads.html for details.
- A subfolder for each sample containing:
- 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.
- 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.
If using both ODT-T RT and N6-T RT primers, two reports are generated, one for statistics from all reads and one for statistics from the N6-T RT primer reads only.
- 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.
- Trimmed reads report (): Summarizes the performed trimming. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_output.html for details.
If using both ODT-T RT and N6-T RT primers, two trimmed reads reports are generated, one for all reads and one for the N6-T RT primer reads only.
Additionally, if using the N6-T RT primer:
- Extract N6-T RT primer reads report (): Summarizes the trimming performed to extract N6-T RT primer reads. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_output.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 (
- Demultiplex report (
- Reads folder:
- Reads (
): A sequence list containing the demultiplexed reads for each sample. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Output_from_Demultiplex_Reads.html for details.
- Reads (
- Tracks folder:
- A subfolder for each sample containing:
- 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.
If using both ODT-T RT and N6-T RT primers, two tracks are generated, one for expression values from all reads and one for expression values from the N6-T RT primer reads only.
- Read mapping (
): The reads mapped to the reference genome.
If using both ODT-T RT and N6-T RT primers, two read mappings are generated, one with all reads and one with the N6-T RT primer reads only. 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 during fusion detection. See also read mapping (fusions) below.
- Unaligned ends (WT) (): The unaligned ends mapped to the reference genome.
- Fusion genes (WT) (
- Fusions:
- 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) (
) , Genes (fusions) (), and mRNA (fusions) (): The reference sequence, gene regions, and mRNA transcripts corresponding to the detected fusions on the artificial fusion chromosomes.
- Fusion genes (fusions) (
- Gene expression (
- A subfolder for each sample containing: