Output from Perform TSO500 RNA Analysis

The Perform TSO500 RNA Analysis (Illumina) workflow produces a relatively large amount of outputs. The outputs have been ordered in a number of folders and single elements as described below.

The two main outputs are:

  1. QC & Reports: A folder that contains the following reports.
    • RNA_remove_and_annotate_with_UMI_report: Contains information about the number of reads being processed and the number and fraction of reads with UMIs.
    • RNA_adapter_trim_report: Summarizes the trimming results such as automatic adapter read-through trimming.
    • RNA_UMI_read_report: A comprehensive report containing statistical metrics and graphical representations on UMI reads. Focus is on duplex, read grouping, read quality and read length distribution.
    • RNA_quality_trim_report: Contains information about quality trimming.
    • RNA-Seq_report: Contains information on mapping statistics.
    • RNA_remove_ligation_artifacts_report: Summarizes ligation and common sequence artifacts found in and removed from the read mapping.
    These reports are summarized in RNA_combined_QC_report, which is useful for quick QC assessment.

  2. Tracks (WT): A folder that contains the following tracks.
    • RNA_read_mapping (WT): The mapping of UMI reads produced by the RNA-Seq Analysis tool
    • Fusion_genes_unaligned_ends (WT): The unaligned ends produced by the RNA-Seq Analysis tool
    • Fusion_genes (WT): The first fusion evidence output from the Detect and Refine Fusion Gene tool. This first evidence builds on mapping of unaligned ends and parameter settings of the tool.
    • Read_mapping_refined (WT): Read mapping from the Detect and Refine Fusion Genes tool, where Fusion chromosomes are removed.
    These elements are presented in the Genome Browser View (WT) together with the VCF Exportable Tracks element described in item 4 and reference elements from the CLC_References location (Reference sequence, Genes, CDS and mRNA). Only the refined read mapping is loaded by default, but the remaining elements can be added for investigating missed fusions.

  3. Tracks (fusion): A folder that contains the fusion chromosome reference tracks and fusion evidence:
    • CDS (fusions) Artificial CDS track matching the artificial reference fusion chromosome
    • Genes (fusions) Artificial genes track matching the artificial reference fusion chromosome
    • mRNA (fusions) Artificial mRNA track matching the artificial reference fusion chromosome
    • RNA_read_mapping (fusions): UMI reads mapped to the artificial fusion chromosomes
    • Fusion_genes (fusion): Fusion gene evidence qualified by mapping evidence to fusion chromosomes
    • Fusion_genes_refined (WT and fusions): Combined track including both fusion gene evidence and evidence qualified by mapping.
    These elements are used in the Genome Browser View (Fusions) that facilitates visualization of the individual fusions.

  4. VCF Exportable Tracks: This folder contains the VCF exportable fusion element called Final_fusion_genes (WT). The track can be exported to VCF format alone or together in a single VCF output together with the VCF Exportable Tracks from the DNA part of the pipeline.