rseqc/rseqc_inner_distance

Description

Calculate inner distance between read pairs.

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_stats: "$id.$key.output_stats"  
output_dist: "$id.$key.output_dist"  
output_freq: "$id.$key.output_freq"  
output_plot: "$id.$key.output_plot"  
output_plot_r: "$id.$key.output_plot_r"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/rseqc/rseqc_inner_distance/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
--sample_size -k	integer	Numer of reads sampled from SAM/BAM file, default = 1000000.
--mapq -q	integer	Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30.
--lower_bound -l	integer	Lower bound of inner distance (bp). This option is used for ploting histograme, default=-250.
--upper_bound -u	integer	Upper bound of inner distance (bp). This option is used for ploting histograme, default=250.
--step -s	integer	Step size (bp) of histograme. This option is used for plotting histogram, default=5.

Name

Type & Properties

--input_file

-i

file

required

--refgene

-r

file

required

--sample_size

-k

integer

--mapq

-q

integer

--lower_bound

-l

integer

--upper_bound

-u

integer

--step

-s

integer

Output

Name	Type & Properties	Description
--output_prefix -o	string required	Rrefix of output files.
--output_stats	file output	output file (txt) with summary statistics of inner distances of paired reads
--output_dist	file output	output file (txt) with inner distances of all paired reads
--output_freq	file output	output file (txt) with frequencies of inner distances of all paired reads
--output_plot	file output	output file (pdf) with histogram plot of of inner distances of all paired reads
--output_plot_r	file output	output file (R) with script of histogram plot of of inner distances of all paired reads

Name

Type & Properties

--output_prefix

-o

string

required

--output_stats

file

output

--output_dist

file

output

--output_freq

file

output

--output_plot

file

output

--output_plot_r

file

output