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Genome Browser Specifications

Process Details

  • Name: Genome Browser
  • Process UUID: yu2zlf7jk5l22jv17ptyu8doh512qj
  • Process Group: Misc.

Overview

This process creates interactive genome browser access files to visualize genomic data including BAM alignments, BED regions, and BigWig tracks. It generates both IGV (Integrative Genomics Viewer) session files and UCSC Genome Browser hub files, enabling researchers to explore their sequencing data in a genomic context with proper track organization and sample grouping.

This process is implemented in Bash, which invokes a Python script for file processing, URL validation, and browser configuration generation.

Key Functionality

  • Multi-format Data Integration: Processes BAM, BED, and BigWig files for comprehensive genomic visualization
  • Sample Grouping: Organizes tracks by experimental conditions when group information is provided
  • Browser Hub Generation: Creates UCSC Genome Browser hub files with proper track hierarchies
  • IGV Session Creation: Generates XML session files for direct loading into IGV with pre-configured tracks

Input/Output Specification

Inputs

Optional Inputs

  • publishBw

    • Description: BigWig files containing signal data for visualization
    • Format: bw

  • group_file

    • Description: Tab-separated file defining sample groupings and experimental conditions
    • Format: tsv

  • bed

    • Description: BED files containing genomic regions of interest
    • Format: bed

  • bamFile

    • Description: BAM alignment files for read visualization
    • Format: bam

  • genome

    • Description: Reference genome FASTA file
    • Format: fasta

Outputs

  • bigWig_file
    • Description: Processed BigWig files organized for browser visualization
    • Format: bigwig

References & Resources

  • Tool Documentation: Contact the team for details on the Python visualization script