Quick Start

A basic RustQC analysis from install to results.

RNA-seq duplicate analysis

Run all RNA-seq QC analyses (dupRadar, featureCounts, RSeQC tools including TIN, Qualimap, preseq, and samtools) in a single pass:

rustqc rna sample.markdup.bam --gtf genes.gtf -p -o results/

This command:

• Analyses sample.markdup.bam against genes.gtf
• Uses paired-end mode (-p)
• Writes all output to results/

Input requirements

• BAM file(s): coordinate-sorted and duplicate-marked (not removed). See CLI reference for supported duplicate-marking tools. The RSeQC tools do not require duplicate marking; this is only needed for the dupRadar analysis. Use --skip-dup-check to bypass the check.
• BAM index: a .bai index is not strictly required, but without one RustQC falls back to a single counting thread. For multi-threaded performance, ensure an index file is present alongside each BAM.
• GTF annotation file (--gtf): a gene annotation file (plain or gzip-compressed). See CLI reference for details.

Output

Output files are organized into subdirectories by tool group. Files are generally named the same as their upstream tool equivalents. This means that MultiQC should find them and report them as if they were created by the original tool. One addition is that RustQC produces SVG versions of all plots.

Use --flat-output to write all files directly to the output directory without subdirectories.

Multiple BAM files

Multiple input files are accepted and processed in parallel, with each producing its own set of output files:

rustqc rna sample1.bam sample2.bam sample3.bam \
  --gtf genes.gtf -p -t 8 -o results/

The annotation file is parsed once and shared across all samples. Threads are distributed automatically among concurrent jobs.