Configuration File

The rustqc rna subcommand supports an optional YAML configuration file for advanced settings that go beyond what CLI flags offer. Pass the config file with --config / -c:

rustqc rna sample.bam --gtf genes.gtf -p -c config.yaml -o results/
# or with BED (RSeQC tools only)
rustqc rna sample.bam --bed genes.bed -p -c config.yaml -o results/

All sections and fields are optional. Missing fields use their default values. Unknown fields are silently ignored, so config files remain forward-compatible.

Note

Since all analyses run within the rustqc rna command, the configuration file controls all tools: dupRadar, featureCounts, and all 7 RSeQC tools. Each RSeQC tool has an enabled toggle and tool-specific parameter overrides. CLI flags take precedence over config file values.

Full example

# Chromosome name remapping
chromosome_prefix: "chr"
chromosome_mapping:
  chrM: "MT"

# dupRadar output toggles
dupradar:
  dup_matrix: true
  intercept_slope: true
  density_scatter_plot: true
  boxplot: true
  expression_histogram: true
  multiqc_intercept: true
  multiqc_curve: true

# featureCounts output toggles
featurecounts:
  counts_file: true
  summary_file: true
  biotype_counts: true
  biotype_counts_mqc: true
  biotype_rrna_mqc: true
  biotype_attribute: "gene_biotype"

# RSeQC tool toggles and settings
bam_stat:
  enabled: true
infer_experiment:
  enabled: true
  sample_size: 200000
read_duplication:
  enabled: true
read_distribution:
  enabled: true
junction_annotation:
  enabled: true
  min_intron: 50
junction_saturation:
  enabled: true
  min_intron: 50
  min_coverage: 1
  percentile_floor: 5
  percentile_ceiling: 100
  percentile_step: 5
inner_distance:
  enabled: true
  sample_size: 1000000
  lower_bound: -250
  upper_bound: 250
  step: 5

# TIN (Transcript Integrity Number)
tin:
  enabled: true
  sample_size: 100
  min_coverage: 10

# Gene body coverage / Qualimap
genebody_coverage:
  enabled: true

# Library complexity (preseq lc_extrap)
preseq:
  enabled: true
  max_extrap: 10000000000
  step_size: 1000000
  n_bootstraps: 100
  confidence_level: 0.95
  seed: 1
  max_terms: 100
  defects: false

# Samtools-compatible outputs
flagstat:
  enabled: true
idxstats:
  enabled: true
samtools_stats:
  enabled: true

Chromosome name mapping

When the chromosome names in your alignment file differ from those in the GTF, RustQC can remap them automatically. Two mechanisms are available, and they can be combined.

chromosome_prefix

A string prefix to prepend to alignment file chromosome names before matching against GTF names. Applied first, before explicit mapping lookups.

# Alignment has "1", "2", "X"; GTF has "chr1", "chr2", "chrX"
chromosome_prefix: "chr"

chromosome_mapping

An explicit mapping from GTF chromosome names (keys) to alignment file chromosome names (values). Applied after the prefix, so explicit entries can override the prefix for specific chromosomes.

# After adding "chr" prefix, override the mitochondrial chromosome
chromosome_mapping:
  chrM: "MT"

A common use case is GENCODE GTFs (which use chr1, chr2, …) with Ensembl alignments (which use 1, 2, …):

chromosome_prefix: "chr"
chromosome_mapping:
  chrM: "MT"

dupRadar output toggles

The dupradar: section controls which dupRadar output files are generated. All outputs are enabled by default.

dupradar:
  dup_matrix: true              # Duplication matrix TSV
  intercept_slope: true         # Intercept/slope fit results
  density_scatter_plot: true    # Density scatter plot (PNG + SVG)
  boxplot: true                 # Duplication rate boxplot (PNG + SVG)
  expression_histogram: true    # Expression histogram (PNG + SVG)
  multiqc_intercept: true       # MultiQC intercept/slope file
  multiqc_curve: true           # MultiQC fitted curve file

Set any field to false to skip generating that output:

dupradar:
  boxplot: false
  expression_histogram: false

featureCounts output toggles

The featurecounts: section controls which featureCounts-compatible output files are generated, plus the biotype attribute setting.

featurecounts:
  counts_file: true           # featureCounts-compatible counts TSV
  summary_file: true          # Assignment summary file
  biotype_counts: true        # Biotype counts TSV
  biotype_counts_mqc: true    # Biotype counts MultiQC bargraph file
  biotype_rrna_mqc: true      # Biotype rRNA percentage MultiQC file
  biotype_attribute: "gene_biotype"  # GTF attribute for biotype grouping

biotype_attribute

The GTF attribute name used for biotype grouping. This controls how genes are categorized in the biotype output files.

GTF source	Typical attribute
Ensembl	gene_biotype
GENCODE	gene_type

Default: "gene_biotype"

This can also be set via the --biotype-attribute CLI flag, which takes precedence over the config file value.

RustQC auto-detects the biotype attribute if the specified one is not found in the GTF. If neither gene_biotype nor gene_type is present, a warning is printed and biotype counting is skipped.

RSeQC tool settings

Each of the 7 RSeQC tools has an enabled toggle (default true) and tool-specific parameter overrides. Disabling a tool here prevents it from running even when annotation is provided. CLI flags take precedence over config file values for all parameters.

bam_stat

bam_stat:
  enabled: true    # Set to false to skip bam_stat

No additional parameters. This tool does not require annotation.

infer_experiment

infer_experiment:
  enabled: true
  sample_size: 200000   # Number of reads to sample (default: 200000)

Requires annotation (--gtf or --bed). The sample_size can also be set via --infer-experiment-sample-size.

read_duplication

read_duplication:
  enabled: true    # Set to false to skip read_duplication

No additional parameters. This tool does not require annotation.

read_distribution

read_distribution:
  enabled: true    # Set to false to skip read_distribution

No additional parameters. Requires annotation (--gtf or --bed).

junction_annotation

junction_annotation:
  enabled: true
  min_intron: 50   # Minimum intron length in bases (default: 50)

Requires annotation (--gtf or --bed). The min_intron can also be set via --min-intron.

junction_saturation

junction_saturation:
  enabled: true
  min_intron: 50           # Minimum intron length in bases (default: 50)
  min_coverage: 1          # Minimum read count to consider a junction (default: 1)
  percentile_floor: 5      # Sampling start percentage (default: 5)
  percentile_ceiling: 100  # Sampling end percentage (default: 100)
  percentile_step: 5       # Sampling step size (default: 5)

Requires annotation (--gtf or --bed). These parameters can also be set via CLI flags: --min-intron, --junction-saturation-min-coverage, --junction-saturation-percentile-floor, --junction-saturation-percentile-ceiling, --junction-saturation-percentile-step.

inner_distance

inner_distance:
  enabled: true
  sample_size: 1000000   # Number of reads to sample (default: 1000000)
  lower_bound: -250      # Histogram lower bound (default: -250)
  upper_bound: 250       # Histogram upper bound (default: 250)
  step: 5                # Histogram bin width (default: 5)

Requires annotation (--gtf or --bed). These parameters can also be set via CLI flags: --inner-distance-sample-size, --inner-distance-lower-bound, --inner-distance-upper-bound, --inner-distance-step.

tin

tin:
  enabled: true
  sample_size: 100     # Equally-spaced positions to sample per transcript (default: 100)
  min_coverage: 10     # Minimum read-start count to compute TIN (default: 10)

Requires annotation (--gtf or --bed). The TIN (Transcript Integrity Number) measures transcript integrity via Shannon entropy of read coverage uniformity.

genebody_coverage

genebody_coverage:
  enabled: true    # Set to false to skip gene body coverage

Requires annotation (--gtf only). Computes coverage profiles along transcript bodies (100 percentile bins, 5’->3’) and produces Qualimap-compatible output.

preseq

preseq:
  enabled: true
  max_extrap: 10000000000  # Maximum extrapolation depth (default: 1e10)
  step_size: 1000000       # Step size between extrapolation points (default: 1e6)
  n_bootstraps: 100        # Bootstrap replicates for confidence intervals (default: 100)
  confidence_level: 0.95   # CI confidence level (default: 0.95)
  seed: 1                  # Random seed for reproducibility (default: 1)
  max_terms: 100           # Maximum terms in power series (default: 100)
  defects: false           # Use defects model for problematic histograms (default: false)

Runs in both GTF and BED modes (only needs BAM fragment info). The max_extrap, step_size, and n_bootstraps can also be set via CLI flags (--preseq-max-extrap, --preseq-step-size, --preseq-n-bootstraps). Use --skip-preseq to disable entirely.

flagstat / idxstats / samtools_stats

flagstat:
  enabled: true        # samtools flagstat-compatible output
idxstats:
  enabled: true        # samtools idxstats-compatible output
samtools_stats:
  enabled: true        # samtools stats SN-section compatible output

These produce samtools-compatible output files in the samtools/ subdirectory. They share the same BAM statistics accumulator as bam_stat — enabling any of them ensures the statistics are collected.