Output from Analyze QIAseq RNA Fusion XP
The following outputs are generated:
- Fusion genes (WT) (
): Breakpoints on the reference genome of all detected fusions.
- Genome browser view (
): 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.
Two browsers are generated, one for wild type (WT) and one for the fusion chromosomes.
- Sample report (
): Sample report containing essential information from all reports produced by the workflow.
- Additionally, if quantifying gene expression:
- Gene expression (
): Track with counts and expression values for each gene.
- Gene expression (
- Additionally, if detecting variants:
- RNA variants (
): Detected variants.
- RNA variants (
- Additionally, if preparing for QCI Interpret:
- QCI Interpret report (): Report prepared for uploading to QCI Interpret and QCI Interpret Translational.
- QCI Interpret report (
- QC & Reports folder:
- Fusion report (
): Summarizes the identified fusions.
- Remove and annotate UMI report (): Summarizes the identified UMIs.
- Remove ligation artifacts report (): Summarizes ligation artifacts found in and removed from the read mapping. Depending on the selected paths, up to two reports are generated, one for the mapping of all reads (named 'Variants') and one for the mapping of 'Fusion' reads only.
- RNA-Seq report (): Summarizes various mapping statistics and biotypes distributions. Depending on the selected paths, up to three reports are generated, one for the RNA-Seq analysis of all reads (named 'Variants'), one for the RNA-Seq analysis of 'Fusion' reads, and one for the RNA-Seq analysis of 'Expression' reads.
- Trim adapters, Trim homopolymers, and Trim on quality reports (): Summarize the performed trimming. The order of these three trimming steps can be seen in the sample report.
- UMI reads report (): Summarizes the UMI reads.
- Additionally, if detecting variants and/or quantifying gene expression:
- QC for RNAscan panels report (): Summarizes various statistics of the mapped reads.
- QC for RNAscan panels report (
- Additionally, if quantifying gene expression:
- rRNA expression report (): Summarizes the percent of the total RNA expression originating from different rRNAs.
- rRNA expression report (
- Fusion report (
- Tracks folder, if detecting variants:
- Amino acid changes (
): Amino acid changes introduced by the detected variants.
- Read mapping (variants) (
): All reads ('Variant', 'Fusion', and 'GEX') mapped to the reference genome..
Furthermore, the output tracks from Detect and Refine Fusion Genes are organized in two subfolders:
- WT subfolder containing:
- Read mapping (WT) (): Reads that mapped best to the reference genome during fusion detection.
- Unaligned ends (WT) (): Unaligned ends mapped to the reference genome.
- Additionally, if detecting variants and/or quantifying gene expression:
- Primers (WT) (): Information about each primer and its read coverage.
- Primers (WT) (
- Read mapping (WT) (
- Fusions subfolder containing:
- Fusion genes (fusions) (): Breakpoints on the artificial fusion chromosomes of all detected fusions.
- Read mapping (fusions) (): Reads that mapped best to the artificial fusion chromosomes during fusion detection.
- Reference sequence (fusions) (
), Genes (fusions) (), mRNA (fusions) (), CDS (fusions) (), and Primers (fusions) (): 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) (
- Amino acid changes (