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Check STAR Files Specifications

Process Details

  • Name: check_STAR_files
  • Process UUID: BKXDJQZnAJEK3AFTu0wSgB7ccHXcQe
  • Process Group: Index

Overview

This process validates the availability and integrity of STAR genome index files required for RNA-seq alignment. It uses a specialized path checking function to verify that the STAR index directory exists and contains the necessary files before proceeding with downstream alignment processes. The process serves as a quality control checkpoint in RNA-seq workflows to prevent pipeline failures due to missing or corrupted index files.

This process is implemented in Bash, which utilizes a custom pathChecker function for file validation.

Key Functionality

  • File Validation: Checks the existence and accessibility of STAR genome index files using the pathChecker function
  • Conditional Execution: Determines whether STAR alignment should proceed based on the run_STAR parameter configuration
  • Quality Control: Provides early detection of missing or corrupted index files to prevent downstream pipeline failures

Input/Output Specification

Inputs

Optional Inputs

  • STAR Index
    • Description: STAR genome index directory containing pre-built index files for alignment
    • Format: starIndex (directory)

Outputs

  • STAR Index
    • Description: Validated STAR genome index directory ready for alignment processes
    • Format: starIndex (directory)

References & Resources

  • Tool Documentation: Contact the team for details on the pathChecker function implementation
  • Related Papers: Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., ... & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21.