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IRFinder BAM Specifications

Process Details

  • Name: IRFinder_BAM
  • Process UUID: f931z8baxfnen1suujb7zxdsq2pi5s
  • Process Group: IRFinder

Overview

This process quantifies intron retention levels from aligned RNA-seq data using IRFinder. It analyzes BAM files to identify and measure intron retention events, which are important for understanding alternative splicing patterns and gene regulation mechanisms in RNA-seq experiments.

This process is implemented in Bash, which invokes IRFinder for intron retention quantification.

Key Functionality

  • Intron Retention Detection: Identifies introns that are retained in mature mRNA transcripts
  • Quantitative Analysis: Measures the extent of intron retention for each detected event
  • BAM File Processing: Processes aligned RNA-seq reads to extract splicing information

Input/Output Specification

Inputs

Required Inputs

  • BAM File

    • Description: Aligned RNA-seq reads in BAM format containing splice junction information
    • Format: BAM

  • Reference

    • Description: IRFinder reference directory containing genome annotation and index files
    • Format: Directory

Outputs

  • IR Results File
    • Description: Tab-delimited file containing intron retention quantification results with retention ratios and statistical measures
    • Format: TXT

Parameters & Settings

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

References & Resources

  • Tool Documentation: Contact the team for details on IRFinder implementation
  • Related Papers: Middleton R, et al. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biol. 2017;18(1):51. doi:10.1186/s13059-017-1184-4