Output from Analyze QIAseq FastSelect and UPXome RNA
The following outputs are generated:
- 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.
If detecting fusions, two browsers are generated, one for wild type and one for the fusion chromosomes.
- Additionally, if preparing for QCI Interpret:
- QCI Interpret report (
): Report prepared for uploading to QCI Interpret and QCI Interpret Translational.
- QCI Interpret report (
- Additionally, for FastSelect:
- Sample report (): Sample report containing essential information from all reports produced by the workflow.
- Sample report (
- Additionally, for UPXome:
- Combined report (
): Combined report containing essential information from all reports produced by the workflow for all samples.
- Gene expression browser (
): An expression browser for inspecting feature expressions, annotations, and statistics for all samples.
If using both ODT-T RT and N6-T RT primers, two browsers are generated, one for gene expressions from all reads and one for gene expressions from the N6-T RT primer reads only.
- PCA plot (
): Principal Component Analysis plot showing the sample-to-sample variation in gene expression.
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.
- Combined report (
- QC & Reports folder:
- QC report (
): Summarizes and visualizes various statistics of the input reads.
- RNA-Seq report (): Summarizes various mapping statistics and biotypes distributions.
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.
- rRNA expression report (): Summarizes the percent of the total RNA expression originating from different rRNAs.
- Trim reads report (): Summarizes the performed read trimming
If using both ODT-T RT and N6-T RT primers, two 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..
- Fusion report (), if detecting fusions: Summarizes the identified fusions.
- Extract N6-T RT primer reads report (
- Additionally, for FastSelect:
- R2 trim reads report. Summarizes the trimming performed to remove the R2 read adapter.
- Additionally, for UPXome:
- Demultiplex report (): Summarizes the number of reads found for each barcode, i.e. for each sample.
- Sample report (): Sample report containing essential information from all reports produced by the workflow.
- Demultiplex report (
- QC report (
- Reads folder (for UPXome only):
- Reads (
): Sequence list containing the demultiplexed reads for each sample.
- Reads (
- Tracks folder:
- Gene expression (
): Track with counts and expression values for each gene.
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 (
): 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.
If detecting fusions, additional output tracks are organized in two subfolders:
- WT:
- Fusion genes (WT) (
): Breakpoints on the reference genome of all detected fusions.
- Read mapping (WT) (): Reads that mapped best to the reference genome during fusion detection. See also read mapping (fusions) below.
- Unaligned ends (WT) (): Unaligned ends mapped to the reference genome.
- Fusion genes (WT) (
- Fusions:
- 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) (), and CDS (fusions) (): Reference sequence, gene regions, mRNA transcripts, and CDS regions corresponding to the detected fusions on the artificial fusion chromosomes.
- Fusion genes (fusions) (
- Gene expression (