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Build Reference IRFinder Specifications

Process Details

  • Name: Build_Reference_IRFinder
  • Process UUID: f931u6vv1imdy7je620e8eko2nlky0
  • Process Group: IRFinder

Overview

This process builds a reference database for IRFinder, a tool designed to detect intron retention events in RNA-seq data. The process prepares the necessary reference files by organizing genomic sequences and gene annotations into the specific directory structure and format required by IRFinder for downstream intron retention analysis.

This process is implemented in Bash, which invokes IRFinder's BuildRefProcess command for reference construction.

Key Functionality

  • Reference Directory Creation: Establishes the required IRFinder reference directory structure
  • File Organization: Renames and positions genome FASTA and GTF annotation files according to IRFinder specifications
  • Reference Database Building: Executes IRFinder's BuildRefProcess to generate the complete reference database for intron retention detection

Input/Output Specification

Inputs

Required Inputs

  • Genome FASTA File

    • Description: Genomic DNA sequences in FASTA format containing all chromosomes/contigs
    • Format: FASTA

  • GTF Annotation File

    • Description: Gene annotation file containing transcript structures, exon boundaries, and gene features
    • Format: GTF

Outputs

  • IRFinder Reference Directory
    • Description: Complete reference database directory containing processed genome sequences, annotations, and IRFinder-specific index files required for intron retention analysis
    • Format: Directory

Parameters & Settings

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

References & Resources

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