rseqc/rseqc_inferexperiment
Description
Infer strandedness from sequencing reads
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 |
Output
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output file (txt) of strandness report. |
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 |
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 Relationships
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Current component
rseqc/rseqc_inferexperimentbiobox v0.3.0
Uses
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