rseqc/rseqc_junctionsaturation

Description

Compare detected splice junctions to reference gene model.

Type

bash_script

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
sampling_percentile_lower_bound: [ 5 ]  
sampling_percentile_upper_bound: [ 100 ]  
sampling_percentile_step: [ 5 ]  
min_intron: [ 50 ]  
min_splice_read: [ 1 ]  
map_qual: [ 30 ]  
output_plot_r: "$id.$key.output_plot_r"  
output_plot: "$id.$key.output_plot"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/rnaseq.git \  
  -revision v0.1.0 \  
  -main-script target/nextflow/rseqc/rseqc_junctionsaturation/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required	input alignment file in BAM or SAM format
--refgene	file required	Reference gene model in bed format
--sampling_percentile_lower_bound	integer	Sampling starts from this percentile, must be an integer between 0 and 100, default =5.
--sampling_percentile_upper_bound	integer	Sampling ends at this percentile, must be an integer between 0 and 100, default =5.
--sampling_percentile_step	integer	Sampling frequency in %. Smaller value means more sampling times. Must be an integer between 0 and 100, default = 5.
--min_intron	integer	Minimum intron length (bp), default = 50.
--min_splice_read	integer	Minimum number of supporting reads to call a junction, default = 1.
--map_qual	integer	Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30.

Name

Type & Properties

--input

file

required

--refgene

file

required

--sampling_percentile_lower_bound

integer

--sampling_percentile_upper_bound

integer

--sampling_percentile_step

integer

--min_intron

integer

--min_splice_read

integer

--map_qual

integer

Output

Name	Type & Properties	Description
--output_plot_r	file output	r script to generate junction_saturation_plot plot
--output_plot	file output	plot of junction saturation (pdf)

Name

Type & Properties

--output_plot_r

file

output

--output_plot

file

output