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RSeQC.md

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The Installation and Usage of RSeQC

1. About

RSeQC is a comprehensive quality control tool for RNA-seq data analysis. It provides a set of modules for assessing various aspects of RNA-seq experiments.

2. Installation and Usage

2.1 Installation

mamba install -c bioconda rseqc

2.2 Basic Usage

Before running RSeQC modules, ensure you have:

  • A sorted and indexed BAM file
  • A reference gene model in BED format

2.3 Key Modules and Commands

  1. Basic Alignment Statistics:

    bam_stat.py -i sample_sorted.bam > bam_stat_output.txt

  2. Read Distribution:

    read_distribution.py -i sample_sorted.bam -r reference.bed > read_distribution_output.txt

  3. Gene Body Coverage:

    geneBody_coverage.py -r reference.bed -i sample_sorted.bam -o gene_body_coverage_output

  4. Infer Experiment:

    infer_experiment.py -i sample_sorted.bam -r reference.bed > infer_experiment_output.txt

  5. Inner Distance:

    inner_distance.py -i sample_sorted.bam -o inner_distance_output -r reference.bed

  6. Junction Saturation:

    junction_saturation.py -i sample_sorted.bam -r reference.bed -o junction_saturation_output

  7. Read Duplication:

    read_duplication.py -i sample_sorted.bam -o read_duplication_output

  8. GC Content:

    read_GC.py -i sample_sorted.bam -o read_GC_output

  9. Read Quality:

    read_quality.py -i sample_sorted.bam -o read_quality_output

  10. Nucleotide Composition:

    read_NVC.py -i sample_sorted.bam -o read_NVC_output