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ATAC MACS Specifications

Process Details

  • Name: ATAC_MACS
  • Process UUID: 20bdd498-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process performs peak calling on ATAC-Seq data using MACS2 (Model-based Analysis of ChIP-Seq). It identifies regions of accessible chromatin by detecting significant peaks in ATAC-Seq sequencing data. The process supports both mouse and human genomes and can handle single or multiple sample inputs with optional control samples.

This process is implemented in Bash, which invokes MACS2 for peak calling and samtools for BAM file processing.

Key Functionality

  • Peak Calling: Uses MACS2 to identify statistically significant peaks in ATAC-Seq data representing accessible chromatin regions
  • Genome Support: Automatically configures genome size parameters for mouse and human genomes
  • Multi-sample Processing: Handles single samples or merges multiple samples for combined peak calling
  • Control Sample Integration: Supports optional control/input samples for improved peak calling accuracy

Input/Output Specification

Inputs

Required Inputs

  • mate

    • Description: Mate pair information for paired-end sequencing data
    • Format: Value parameter

  • bam_file

    • Description: Aligned sequencing reads in BAM format from ATAC-Seq experiment
    • Format: BAM file

  • bed

    • Description: Genomic intervals in BED format for peak calling analysis
    • Format: BED file

  • name

    • Description: Sample or experiment identifier for output file naming
    • Format: Text value

Outputs

  • bed

    • Description: Peak regions identified by MACS2 in BED format
    • Format: BED file

  • bam_file

    • Description: Processed BAM file(s), merged if multiple samples were provided
    • Format: BAM file set

  • compare_bed

    • Description: Comparison BED file for downstream analysis
    • Format: BED comparison file

  • resultsdir

    • Description: Complete results directory containing all MACS2 output files including peaks, summits, and statistical information
    • Format: Results directory

References & Resources

  • Tool Documentation: Contact the team for details on MACS2 implementation and parameters
  • Related Papers: Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biology 9, R137 (2008). DOI: 10.1186/gb-2008-9-9-r137