rustqc/rustqc_rna

RNA-seq

quality control

RSeQC

featureCounts

dupRadar

Qualimap

preseq

samtools

Description

RNA-Seq QC — single-pass analysis of BAM/SAM/CRAM files.

Runs featureCounts, dupRadar, Qualimap, samtools stats, and RSeQC analyses
(infer_experiment, read_distribution, junction_annotation, junction_saturation,
inner_distance, read_duplication, TIN, bam_stat) in one pass over the input file.
Requires a GTF annotation and duplicate-marked (not removed) alignments.

Documentation

Type

bash_script

License

GPL-3.0

Keywords

RNA-seq

quality control

RSeQC

featureCounts

dupRadar

Qualimap

preseq

samtools

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
outdir: "$id.$key.outdir.qc_results"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/rustqc/rustqc_rna/main.nf \  
  -params-file params.yaml

Input / Output

Name	Type & Properties	Description
--input	file required multiple	Duplicate-marked alignment file(s) in SAM, BAM, or CRAM format. Multiple files can be provided and will be processed together.
--gtf -g	file required	GTF gene annotation file, plain or gzip-compressed.
--reference -r	file	Reference FASTA file. Required when input is in CRAM format.
--outdir -o	file required output	Output directory for all QC result files. Defaults to the current directory.
--sample_name	string	Override the sample name used for output filenames. Defaults to the BAM filename.
--flat_output	boolean_true	Write all output files directly into the output directory without subdirectories.
--config -c	file	YAML configuration file for RustQC tool parameters.
--json_summary -j	string	Path for the JSON summary output. Use `-` to write to stdout.

Name

Type & Properties

--input

file

required

multiple

--gtf

-g

file

required

--reference

-r

file

--outdir

-o

file

required

output

--sample_name

string

--flat_output

boolean_true

--config

-c

file

--json_summary

-j

string

Library

Name	Type & Properties	Description
--stranded -s	string	Library strandedness for read counting and RSeQC analyses. - `unstranded`: reads are counted on either strand - `forward`: read 1 maps to the transcript strand (e.g. ligation-based) - `reverse`: read 2 maps to the transcript strand (e.g. dUTP)
--paired -p	boolean_true	Input reads are paired-end.

Name

Type & Properties

--stranded

-s

string

--paired

-p

boolean_true

General

Name	Type & Properties	Description
--mapq -Q	integer	MAPQ cutoff for quality filtering. Reads below this threshold are excluded. Default: `30`.
--biotype_attribute	string	GTF attribute name used for biotype grouping in featureCounts summaries.
--skip_dup_check	boolean_true	Skip the check that verifies input alignments are duplicate-marked.
--quiet -q	boolean_true	Suppress all output except warnings and errors.
--verbose -v	boolean_true	Show additional detail during processing.

Name

Type & Properties

--mapq

-Q

integer

--biotype_attribute

string

--skip_dup_check

boolean_true

--quiet

-q

boolean_true

--verbose

-v

boolean_true

Tool parameters

Name	Type & Properties	Description
--infer_experiment_sample_size	integer	Number of reads sampled for strandedness inference. Default: `200000`.
--min_intron	integer	Minimum intron size for junction annotation. Default: `50`.
--junction_saturation_seed	integer	Random seed for reproducible junction saturation results.
--junction_saturation_min_coverage	integer	Minimum read coverage for a junction to be included in saturation analysis. Default: `1`.
--junction_saturation_percentile_floor	integer	Starting subsampling percentage for junction saturation analysis. Default: `5`.
--junction_saturation_percentile_ceiling	integer	Ending subsampling percentage for junction saturation analysis. Default: `100`.
--junction_saturation_percentile_step	integer	Step size between subsampling percentages for junction saturation. Default: `5`.
--inner_distance_sample_size	integer	Number of read pairs sampled for inner distance estimation. Default: `1000000`.
--inner_distance_lower_bound	integer	Lower bound for inner distance histogram. Default: `-250`.
--inner_distance_upper_bound	integer	Upper bound for inner distance histogram. Default: `250`.
--inner_distance_step	integer	Bin width for inner distance histogram. Default: `5`.
--tin_seed	integer	Random seed for reproducible TIN (Transcript Integrity Number) results.
--skip_tin	boolean_true	Skip TIN (Transcript Integrity Number) analysis.
--skip_read_duplication	boolean_true	Skip read duplication analysis.
--skip_preseq	boolean_true	Skip preseq library complexity analysis.
--preseq_seed	integer	Random seed for preseq bootstrap confidence intervals. Default: `408`.
--preseq_max_extrap	long	Maximum extrapolation depth for preseq. Default: `1e10`.
--preseq_step_size	integer	Step size between extrapolation points for preseq. Default: `1e6`
--preseq_n_bootstraps	integer	Number of bootstrap replicates for preseq confidence intervals. Default: `100`.
--preseq_seg_len	integer	Maximum segment length for paired-end merging in preseq. Default: `1e8`.

Name

Type & Properties

--infer_experiment_sample_size

integer

--min_intron

integer

--junction_saturation_seed

integer

--junction_saturation_min_coverage

integer

--junction_saturation_percentile_floor

integer

--junction_saturation_percentile_ceiling

integer

--junction_saturation_percentile_step

integer

--inner_distance_sample_size

integer

--inner_distance_lower_bound

integer

--inner_distance_upper_bound

integer

--inner_distance_step

integer

--tin_seed

integer

--skip_tin

boolean_true

--skip_read_duplication

boolean_true

--skip_preseq

boolean_true

--preseq_seed

integer

--preseq_max_extrap

long

--preseq_step_size

integer

--preseq_n_bootstraps

integer

--preseq_seg_len

integer