rseqc/rseqc_inner_distance
Description
Calculate inner distance between read pairs.
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. |
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 |
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 v0.4.1 \
-main-script target/nextflow/rseqc/rseqc_inner_distance/main.nf \
-params-file params.yaml Relationships
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Current component
rseqc/rseqc_inner_distancebiobox v0.4.1
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