Description

Run post-alignment QC tools on RNA-seq BAM files including library complexity estimation (Preseq), biotype QC (featureCounts), RNA-seq-specific QC metrics (Qualimap), duplicate rate analysis (dupRadar), and comprehensive RSeQC analysis.

Input

name
description
pattern

ch_bam_bai

Coordinate-sorted BAM file aligned to the genome, with its index.

Structure: [ val(meta), path(bam), path(bai) ]

*.{bam,bai}

ch_gtf

GTF annotation file.

Structure: [ val(meta), path(gtf) ]

*.{gtf}

ch_gene_bed

BED12 file for the reference gene model.

Structure: [ path(bed) ]

*.{bed}

ch_fasta_fai

FASTA reference and its index, used by samtools sort.

Structure: [ val(meta), path(fasta), path(fai) ]

ch_biotypes_header

Header file for the biotype counts MultiQC section.

Structure: [ val(meta), path(biotypes_header.txt) ]

*.{txt}

tools

List of QC tools to run. Top-level tools: ‘preseq’, ‘biotype_qc’, ‘qualimap’,
‘dupradar’. RSeQC modules use an ‘rseqc_’ prefix: ‘rseqc_bam_stat’,
‘rseqc_inner_distance’, ‘rseqc_infer_experiment’, ‘rseqc_junction_annotation’,
‘rseqc_junction_saturation’, ‘rseqc_read_distribution’, ‘rseqc_read_duplication’,
‘rseqc_tin’. Pass an empty list to skip all.

biotype

GTF attribute for biotype grouping (e.g. “gene_type” or “gene_biotype”).
Only used when ‘biotype_qc’ is in tools. Set to empty string to skip biotype QC.

Output

name
description
pattern

multiqc_files

Collected MultiQC-compatible output files from all enabled tools.

Structure: [ val(meta), path(files) ]

preseq_lc_extrap

Preseq library complexity extrapolation curve.

Structure: [ val(meta), path(txt) ]

*.lc_extrap.txt

preseq_log

Preseq log file.

Structure: [ val(meta), path(log) ]

*.log

featurecounts_counts

featureCounts count matrix.

Structure: [ val(meta), path(txt) ]

*.featureCounts.txt

featurecounts_summary

featureCounts summary statistics.

Structure: [ val(meta), path(txt) ]

*.featureCounts.txt.summary

biotype_tsv

Biotype counts formatted for MultiQC bargraph.

Structure: [ val(meta), path(tsv) ]

*biotype_counts_mqc.tsv

biotype_rrna

rRNA percentage for MultiQC general stats.

Structure: [ val(meta), path(tsv) ]

*biotype_counts_rrna_mqc.tsv

qualimap_results

Qualimap RNA-seq QC results directory.

Structure: [ val(meta), path(dir) ]

dupradar_scatter2d

PDF duplication rate against total read count plot.

Structure: [ val(meta), path(pdf) ]

*_duprateExpDens.pdf

dupradar_boxplot

PDF duplication rate ~ total reads per kilobase (RPK) boxplot.

Structure: [ val(meta), path(pdf) ]

*_duprateExpBoxplot.pdf

dupradar_hist

PDF expression histogram.

Structure: [ val(meta), path(pdf) ]

*_expressionHist.pdf

dupradar_dupmatrix

Text file containing tags falling on the features described in the GTF file.

Structure: [ val(meta), path(txt) ]

*_dupMatrix.txt

dupradar_intercept_slope

Text file containing intercept and slope from dupRadar modelling.

Structure: [ val(meta), path(txt) ]

*_intercept_slope.txt

dupradar_multiqc

dupRadar MultiQC-compatible output.

Structure: [ val(meta), path(txt) ]

*_mqc.txt

inferexperiment_txt

RSeQC infer_experiment results (for strandedness detection).

Structure: [ val(meta), path(txt) ]

*.infer_experiment.txt

bamstat_txt

RSeQC bam_stat report.

Structure: [ val(meta), path(txt) ]

*.bam_stat.txt

innerdistance_all

All the output files from RSeQC inner_distance.

Structure: [ val(meta), path(txt/pdf/r) ]

*.{txt,pdf,R}

innerdistance_distance

The inner distances.

Structure: [ val(meta), path(txt) ]

*.inner_distance.txt

innerdistance_freq

Frequencies of different insert sizes.

Structure: [ val(meta), path(txt) ]

*.inner_distance_freq.txt

innerdistance_mean

Mean/median values of inner distances.

Structure: [ val(meta), path(txt) ]

*.inner_distance_mean.txt

innerdistance_pdf

Distribution plot of inner distances.

Structure: [ val(meta), path(pdf) ]

*.inner_distance_plot.pdf

innerdistance_rscript

Script to reproduce the inner distance plot.

Structure: [ val(meta), path(r) ]

*.inner_distance_plot.R

junctionannotation_all

All the output files from RSeQC junction_annotation.

Structure: [ val(meta), path(bed/xls/pdf/r/log) ]

*.{bed,xls,pdf,R,log}

junctionannotation_bed

BED file of annotated junctions.

Structure: [ val(meta), path(bed) ]

*.junction.bed

junctionannotation_interact_bed

Interact BED file.

Structure: [ val(meta), path(bed) ]

*.Interact.bed

junctionannotation_xls

XLS file with junction information.

Structure: [ val(meta), path(xls) ]

*.xls

junctionannotation_pdf

Junction plot.

Structure: [ val(meta), path(pdf) ]

*.junction.pdf

junctionannotation_events_pdf

Events plot.

Structure: [ val(meta), path(pdf) ]

*.events.pdf

junctionannotation_rscript

Rscript to reproduce the junction annotation plots.

Structure: [ val(meta), path(r) ]

*.r

junctionannotation_log

Log file generated by RSeQC junction_annotation.

Structure: [ val(meta), path(log) ]

*.log

junctionsaturation_all

All the output files from RSeQC junction_saturation.

Structure: [ val(meta), path(pdf/r) ]

*.{pdf,R}

junctionsaturation_pdf

Junction saturation report.

Structure: [ val(meta), path(pdf) ]

*.pdf

junctionsaturation_rscript

Junction saturation R-script.

Structure: [ val(meta), path(r) ]

*.r

readdistribution_txt

RSeQC read_distribution report.

Structure: [ val(meta), path(txt) ]

*.read_distribution.txt

readduplication_all

All the output files from RSeQC read_duplication.

Structure: [ val(meta), path(xls/pdf/r) ]

*.{xls,pdf,R}

readduplication_seq_xls

Read duplication rate determined from the sequence of the read.

Structure: [ val(meta), path(xls) ]

*seq.DupRate.xls

readduplication_pos_xls

Read duplication rate determined from the mapping position of the read.

Structure: [ val(meta), path(xls) ]

*pos.DupRate.xls

readduplication_pdf

Plot of duplication rate.

Structure: [ val(meta), path(pdf) ]

*.pdf

readduplication_rscript

Script to reproduce the duplication rate plot.

Structure: [ val(meta), path(r) ]

*.R

tin_txt

RSeQC TIN results summary.

Structure: [ val(meta), path(txt) ]

*.txt

per_sample_mqc_bundle

Per-sample MultiQC-feeding outputs (Preseq, biotype TSV, Qualimap,
dupRadar, and RSeQC bamstat/inferexperiment/innerdistance_freq/
junctionannotation_log/junctionsaturation_rscript/readdistribution/
readduplication_pos/tin) joined on meta.

Structure: [ val(meta), list(files) ]

included in
rnaseq
included modules and subworkflows
preseq/lcextrapqualimap/rnaseqdupradar and 4 more modules
maintainer
Github user pinin4fjords
get in touch
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