rseqc/rseqc_inferexperiment

Description

Infer strandedness from sequencing reads

Type

bash_script

License

GPL-3.0

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/rseqc/rseqc_inferexperiment/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input_file -i	file required	input alignment file in BAM or SAM format
--refgene -r	file required	Reference gene model in bed format

Name

Type & Properties

--input_file

-i

file

required

--refgene

-r

file

required

Output

Name	Type & Properties	Description
--output	file required output	Output file (txt) of strandness report.

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--sample_size -s	integer	Number of reads sampled from SAM/BAM file. Default: 200000
--mapq -q	integer	Minimum mapping quality (phred scaled) to determine uniquely mapped reads. Default: 30

Name

Type & Properties

--sample_size

-s

integer

--mapq

-q

integer