Output from the Perform QIAseq RNA Fusion XP 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.
- 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.
Two browsers are generated, one for wild type (WT) and one for the fusion chromosomes.
- PASS fusion genes (WT) (
): The breakpoints on the artificial fusion chromosomes 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.
- RNA variants passing filters (
): The RNA variants that have passed all relevant filters. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Variant_tracks.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 (
): A graphical report of the fusions found in the sample. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Output_from_Detect_Refine_Fusion_Genes_tool.html for details.
- QC report (): Summarizes various statistics of the mapped reads. Two reports are generated, one for the mapping of all reads and one for the mapping of 'Fusion' reads only.
See The QIAseq RNAscan Panels Report for details.
- Remove and annotate UMI report (): Summarizes the identified UMIs. See Remove and Annotate with Unique Molecular Index for details.
- Remove ligation artifacts report (): Summarizes ligation artifacts found in and removed from the read mapping. Two reports are generated, one for the mapping of all reads and one for the mapping of 'Fusion' reads only. See Remove Ligation Artifacts for details.
- RNA-Seq report (): Summarizes various mapping statistics and biotypes distributions. Three reports are generated, one for the RNA-Seq analysis of all reads, one for the RNA-Seq analysis of 'Fusion' reads, and one for the RNA-Seq analysis of 'Expression' reads.
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.
- umiFromReadsReportOutput. See Create UMI Reads from Reads for details.
- Fusion report (
- Tracks folder:
- Amino acid track (
): A graphical representation of the amino acid changes.
The track is based on the CDS track and in addition to the amino acid sequence of the coding sequence, all amino acids that have been affected by variants are shown as individual amino acids below the amino acid track. Changes causing a frameshift are symbolized with two arrow heads, and variants causing premature stop are marked with an asterisk. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Amino_Acid_Changes.html for details.
- Read mapping (Variants) (
): Mapping of all reads ('Variant', 'Fusion', and 'GEX') to the reference genome. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_result_handling.html for details.
- RNA unfiltered variants (): The variants identified before filtering. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Variant_tracks.html for details.
Furthermore, the output tracks from Detect and Refine Fusion Genes are organized in two subfolders:
- WT:
- Fusion genes (WT) (): The breakpoints on the reference genome of all detected fusions.
- Primers (WT) (): The panel primer regions on the reference genome.
- 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) (), CDS (fusions) (), and Primers (fusions) (): The reference sequence, gene regions, mRNA transcripts, CDS regions, and panel primer 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) (
- Amino acid track (