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Check BED12 Specifications

Process Details

  • Name: Check BED12
  • Process UUID: 17fc78a6-e169-11e9-be30-e0aab38271b1
  • Process Group: File Conversions

Overview

This process converts GTF (Gene Transfer Format) files to BED12 format or validates existing BED12 files. It checks if a BED12 file already exists at the specified location and either uses the existing file or generates a new one from the input GTF file using the GTF2BED12 conversion tool.

This process is implemented in Bash, which invokes a Perl script for GTF to BED12 format conversion.

Key Functionality

  • Format Validation: Checks for the existence of BED12 files at specified paths
  • GTF to BED12 Conversion: Converts GTF annotation files to BED12 format when needed
  • File Management: Handles file copying and directory creation for organized output storage

Input/Output Specification

Inputs

Required Inputs

  • GTF File
    • Description: Gene annotation file in GTF format containing gene structure information
    • Format: GTF

Outputs

  • BED12 File
    • Description: Gene annotation file in BED12 format suitable for genome browsers and downstream analysis
    • Format: BED

References & Resources

  • Tool Documentation: Contact the team for details on the GTF2BED12 conversion script