Skip to content

ATAC Prep Specifications

Process Details

  • Name: ATAC_Prep
  • Process UUID: 20bdd434-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

ATAC Prep is a preprocessing process for ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data analysis. This process converts BAM alignment files to BED format and performs critical adjustments to account for the transposase cutting mechanism by shifting cut sites by 9 bases to center on the actual binding sites.

This process is implemented in Bash, utilizing Bedtools v2.25.0 for genomic interval operations.

Key Functionality

  • BAM to BED Conversion: Converts aligned sequencing reads from BAM format to BED format for downstream peak calling and analysis
  • Cut Site Adjustment: Shifts ATAC-seq cut sites by 9 bases to accurately represent transposase binding locations, accounting for the 5' offset introduced during library preparation
  • Strand-Specific Processing: Handles positive and negative strand reads differently to ensure proper cut site positioning and generates 29-base pair windows around adjusted cut sites

Input/Output Specification

Inputs

Required Inputs

  • Mate Information

    • Description: Paired-end sequencing mate designation
    • Format: Value parameter

  • Mapped Reads

    • Description: Aligned sequencing reads from ATAC-seq experiment
    • Format: BAM files

  • Genome Sizes

    • Description: Chromosome sizes file for the reference genome used in alignment
    • Format: Sizes file

Outputs

  • BED File

    • Description: Processed BED file with adjusted cut sites representing transposase binding locations
    • Format: BED format

  • BAM File

    • Description: Original BAM alignment file organized in output directory structure
    • Format: BAM format

  • Sample Name

    • Description: Sample identifier for tracking and downstream analysis
    • Format: Name value

Parameters & Settings

This process uses conditional execution based on ATAC-seq MACS2 pipeline settings configured elsewhere in the workflow.

References & Resources

  • Tool Documentation: Contact the team for details on the ATAC-seq preprocessing pipeline
  • Related Papers: Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., and Greenleaf, W.J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods 10, 1213-1218.