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DNA-Seq QC Metrics


The DNA-Seq QC Metrics module will run multiple QC commands simultaneously, without having to go through each individual menu presenting the results in a table format.

To access this module, please go to Analysis | NGS | Aligned Data QC | DNA-Seq QC Metrics

DNAseqQC Menu.png

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Input Data Requirements

This module works on aligned DNA-seq .bam files, such as from the Map DNA-seq Reads to the Genome module. You can also run this module on DNA-seq .bam files that have been added to Array Studio by Add Genome-Mapped Reads.

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General Options



  • Project: Specify the project to run the QC analysis.
  • Data: Specify NGS data to run the QC analysis.
  • References: Run on "All references", "Customized references", or a "Filtered by region" set of references. In most cases, references will be chromosomes.
  • Observations: The module can also be run on "All observations", "Visible observations", "Selected observations", or "Customized observations".
  • Output Type: The data type that results from this module.
  • Output name: An output name can be specified for the report.
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  • Gene model - Select the Gene model to be used for mapping the sequences.
  • Job number - The total number of jobs to run in parallel.

  • Exclude duplicate alignments: Only one read in a set of duplicated aligned reads will be counted. Duplicates are identified by the duplication flag.
  • Exclude failed alignments - Reads with flag "ReadIsFailed" will be excluded. See also FLAG
  • Exclude secondary alignments - Only the primary read alignment will be used in the QC metrics (OSA randomly flag one of the ties as primary while others as secondary).
  • Exclude multi-reads (ZC tag required) - Multi reads are considered non-unique (i.e. reads that align to multiple genomic locations with equal or similar numbers of mismatches). Selecting this option will include unique reads only when performing the SNP summarization.
  • Exclude singletons (paired end required) - Will not count reads where both pairs did not map to the same region.

  • QC Metrics - Select the desired metrics to appear in the resulting report.
    • Metrics are grouped by the categories displayed here.
  • Output folder - An output folder can be specified for the report.
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Output Results

This module will output a table containing metrics under the selected categories. Depending on the results, you can spot potential problematic or failed experiments, or indications to change your DNA-seq mapping parameters.

DNASeq QC Metrics Table

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