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RSEM Alignment Summary Specifications

Process Details

  • Name: RSEM Alignment Summary
  • Process UUID: 17fc5b78-e169-11e9-be30-e0aab38271b1
  • Process Group: Misc.

Overview

This process generates a comprehensive summary of RSEM alignment results by extracting key alignment statistics from RSEM output files. It processes multiple samples simultaneously and compiles alignment metrics including total reads, multimapped reads aligned, and unique aligned reads into a standardized TSV format for downstream analysis and quality assessment.

This process is implemented in Bash, which invokes a Perl script for parsing RSEM statistics files and generating the summary report.

Key Functionality

  • Statistics Extraction: Parses RSEM output files to extract alignment statistics from .cnt files for each sample
  • Multi-sample Processing: Automatically processes all RSEM output directories in the working directory
  • Alignment Metrics Calculation: Computes total reads, multimapped reads, and unique aligned reads for each sample
  • Summary Report Generation: Compiles all statistics into a single TSV file with standardized headers

Input/Output Specification

Inputs

Required Inputs

  • RSEM Output
    • Description: Directory structure containing RSEM alignment results with statistics files
    • Format: rsemOut (RSEM output directory structure)

Outputs

  • Alignment Summary Report
    • Description: Tab-separated values file containing alignment statistics for all processed samples including total reads, multimapped reads aligned, and unique aligned reads
    • Format: TSV

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on the Perl parsing script
  • Related Papers: Li, B., & Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics, 12(1), 323.