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.
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. |
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. |
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. |
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 v0.4.2 \
-main-script target/nextflow/qualimap/qualimap_rnaseq/main.nf \
-params-file params.yaml Relationships
Used by
3 relationships, 2 components
Current component
qualimap/qualimap_rnaseqbiobox v0.4.2
Uses
0 relationships
No component dependencies found.