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STAR Summary Specifications

Process Details

  • Name: STAR Summary
  • Process UUID: 20bdce8a-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process merges STAR alignment output files into a single summary table file. It aggregates alignment statistics from multiple STAR output files and creates a comprehensive summary report showing total reads, uniquely mapped reads, and multimapped reads for each sample.

This process is implemented in Bash, which invokes a Perl script for data aggregation and summary table generation.

Key Functionality

  • STAR Output Aggregation: Parses multiple STAR alignment log files to extract key alignment statistics
  • Read Count Summarization: Calculates total input reads, uniquely mapped reads, and multimapped reads across samples
  • Summary Table Generation: Creates a consolidated TSV file with alignment statistics for downstream analysis and reporting

Input/Output Specification

Inputs

Required Inputs

  • STAR Output Files
    • Description: Collection of STAR alignment log files containing alignment statistics
    • Format: STAR log files (out format)

Outputs

  • Summary Table

    • Description: Consolidated alignment statistics table containing sample names, total reads, multimapped reads, and uniquely aligned reads
    • Format: TSV (Tab-separated values)

  • Process Name

    • Description: Name identifier for the summary process
    • Format: Text string

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 aggregation script
  • Related Papers: Dobin, A., Davis, C. A., Schlesinger, F., et al. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21. https://doi.org/10.1093/bioinformatics/bts635