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RSeQC Summary Specifications

Process Details

  • Name: RSeQC Summary
  • Process UUID: 20bdcc78-ed05-11e8-9ce4-85221b21564c
  • Process Group: QC

Overview

This process generates comprehensive summary statistics from RSeQC (RNA-seq Quality Control) output files, providing essential quality metrics for RNA-seq data analysis. The process creates separate TSV files containing counts and tags per kilobase (kb) statistics for various genomic regions including CDS exons, UTR regions, introns, and transcription start/end site flanking regions.

This process is implemented in Perl.

Key Functionality

  • RSeQC Output Parsing: Processes RSeQC output files to extract read distribution statistics across different genomic regions
  • Multi-Region Analysis: Analyzes reads mapping to CDS exons, 5'UTR exons, 3'UTR exons, introns, and regulatory regions around transcription start sites (TSS) and transcription end sites (TES)
  • Dual Output Generation: Creates both raw count files and normalized tags per kilobase files for comprehensive quality assessment

Input/Output Specification

Inputs

Required Inputs

  • outputFileOut

    • Description: RSeQC output files containing read distribution statistics
    • Format: .out files

  • mate

    • Description: Mate pair information for the sequencing data
    • Format: mate value

Outputs

  • outputFileTSV
    • Description: Summary statistics in tabular format containing counts and tags per kilobase for genomic regions
    • Format: TSV files (.counts.tsv and .tagskb.tsv)

Parameters & Settings

This process uses predefined parameters for genomic region analysis and does not have user-configurable parameters in the Foundry UI.

References & Resources

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