qualimap/qualimap_rnaseq

RNA-seq

quality control

QC Report

Description

Qualimap RNA-seq QC reports quality control metrics and bias estimations
which are specific for whole transcriptome sequencing, including reads genomic
origin, junction analysis, transcript coverage and 5’-3’ bias computation.

Type

bash_script

License

GPL-2.0

Keywords

RNA-seq

quality control

QC Report

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
qc_results: "$id.$key.qc_results.txt"  
counts: "$id.$key.counts"  
report: "$id.$key.report.html"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.2.0 \  
  -main-script target/nextflow/qualimap/qualimap_rnaseq/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--bam	file required	Path to the sequence alignment file in BAM format, produced by a splicing-aware aligner.
--gtf	file required	Path to genomic annotations in Ensembl GTF format.

Name

Type & Properties

--bam

file

required

--gtf

file

required

Output

Name	Type & Properties	Description
--qc_results	file required output	Text file containing the RNAseq QC results.
--counts	file output	Output file for computed counts.
--report	file output	Report output file. Supported formats are PDF or HTML.

Name

Type & Properties

--qc_results

file

required

output

--counts

file

output

--report

file

output

Optional

Name	Type & Properties	Description
--num_pr_bases	integer	Number of upstream/downstream nucleotide bases to compute 5'-3' bias (default = 100).
--num_tr_bias	integer	Number of top highly expressed transcripts to compute 5'-3' bias (default = 1000).
--algorithm	string	Counting algorithm (uniquely-mapped-reads (default) or proportional).
--sequencing_protocol	string	Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).
--paired	boolean_true	Setting this flag for paired-end experiments will result in counting fragments instead of reads.
--sorted	boolean_true	Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis.
--java_memory_size	string	maximum Java heap memory size, default = 4G.

Name

Type & Properties

--num_pr_bases

integer

--num_tr_bias

integer

--algorithm

string

--sequencing_protocol

string

--paired

boolean_true

--sorted

boolean_true

--java_memory_size

string