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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
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.
- 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.
- 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.
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.