Skip to content

IRFinder Diff Specifications

Process Details

  • Name: IRFinder Diff
  • Process UUID: f9311qixuf4qsnbygqtkubfsu7p5jj
  • Process Group: IRFinder

Overview

This process performs differential intron retention analysis by comparing control and treatment samples. It identifies statistically significant differences in intron retention levels between experimental conditions, providing insights into alternative splicing patterns and their potential functional implications.

This process is implemented in Bash, which executes the IRFinder Diff command-line tool for statistical comparison of intron retention events.

Key Functionality

  • Differential Analysis: Compares intron retention levels between control and treatment groups using statistical methods
  • Batch Processing: Automatically processes multiple sample files from control and treatment directories
  • Statistical Testing: Performs appropriate statistical tests to identify significantly different intron retention events
  • Results Organization: Generates organized output files containing differential analysis results

Input/Output Specification

Inputs

Required Inputs

  • inputDir
    • Description: Directory containing subdirectories with IRFinder results from control and treatment samples, including IR.txt files for each sample
    • Format: Directory

Outputs

  • inputDir
    • Description: Directory containing the original input data plus a new subdirectory with differential analysis results showing significantly different intron retention events between conditions
    • Format: Directory

Parameters & Settings

This process uses default parameters for the IRFinder Diff analysis. No user-configurable parameters are available in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on IRFinder Diff analysis parameters and output interpretation