Output from the Perform QIAseq FastSelect RNA Analysis workflow
The following outputs are generated:
- Fusion genes (fusions) (
), if running fusion detection: The breakpoints on the artificial fusion chromosomes of all detected fusions. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Output_from_Detect_Refine_Fusion_Genes_tool.html for details.
- 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 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.
- 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:
- 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.
- R2 trimming and Trimmed reads reports (): Summarize 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.
- 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.
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 (
- Tracks folder:
- Read mapping (
): The reads mapped to the reference genome. 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 mappings are generated, one for the mapping of all reads and one for the mapping of N6-T RT primer reads only.
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:
- 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.
- Read mapping (fusions) (
- Read mapping (