Output from Analyze QIAseq RNAscan
The following outputs are generated:
- Fusion genes (WT) (
): Breakpoints on the reference genome of all detected fusions.
- Gene expression (
): Track with counts and expression values for each gene.
- 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 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.
- QC for RNAscan panels report (): Summarizes various statistics of the mapped reads.
- QC report (): Summarizes and visualizes various statistics of the input reads.
- Remove and annotate UMI report (): Summarizes the identified UMIs.
- Remove ligation artifacts report (): Summarizes ligation artifacts found in and removed from the read mapping.
- RNA-Seq report (): Summarizes various mapping statistics and biotypes distributions.
- rRNA expression report (): Summarizes the percent of the total RNA expression originating from different rRNAs.
- 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.
- Fusion report (
- Tracks folder:
- Panel primers (): Information about each primer and its read coverage. See QC for RNAscan Panels for details.
- Read mapping (
): Reads mapped to the reference genome.
- 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.
- 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) (
- Panel primers (