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RSeQC Specifications

Process Details

  • Name: RSeQC
  • Process UUID: 20bdb2c4-ed05-11e8-9ce4-85221b21564c
  • Process Group: QC

Overview

RSeQC is a quality control process that analyzes the distribution of mapped RNA-seq reads across different genomic features. This module calculates how mapped reads are distributed over genome features including CDS exons, 5' UTR exons, 3' UTR exons, introns, and intergenic regions. It provides essential quality metrics for RNA-seq data analysis by assessing read mapping patterns and experimental design validation.

This process is implemented in Bash, which invokes Python scripts from the RSeQC package for read distribution analysis and experimental inference.

Key Functionality

  • Read Distribution Analysis: Calculates the proportion of mapped reads falling into different genomic regions (exons, introns, UTRs, intergenic regions)
  • Experimental Design Inference: Determines the strandedness of the RNA-seq library preparation protocol
  • Quality Assessment: Provides metrics to evaluate the success of RNA-seq mapping and library preparation

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads

    • Description: BAM files containing aligned RNA-seq reads
    • Format: BAM

  • Gene Annotation

    • Description: BED format file containing gene model annotations for genomic feature classification
    • Format: BED

Outputs

  • Quality Control Report
    • Description: Text files containing read distribution statistics and experimental inference results
    • Format: OUT

Parameters & Settings

This process runs automatically when quality control is enabled in the pipeline configuration.

References & Resources

  • Tool Documentation: Contact the team for details on read_distribution.py and infer_experiment.py
  • Related Papers: Wang, L., Wang, S., & Li, W. (2012). RSeQC: quality control of RNA-seq experiments. Bioinformatics, 28(16), 2184-2185. https://doi.org/10.1093/bioinformatics/bts356