Home
    • Project overview
    • Policies
    • News
    • Contact
    • Experiments
    • Annotations
    • Single Cell Embeddings
    • Statistical Models
    • Gene Perturbations
    • Data Standards & QC
    • Pipelines
    • Consortia
    • Publications
    • Single Cell Browser
    • Getting started
    • Schema
Clear Filters
Assay
  • 2ChIP-seq
  • 2Mint-ChIP-seq
  • 1ATAC-seq
Pipeline status
  • 1active
Pipeline groups
  • 1ATAC-seq Pipeline (ENCODE replicated)
Software
  • 7MACS2
  • 6BEDTools
  • 6Samtools
  • 5Picard
  • 4Bowtie 2
  • 2BWA
  • 2Irreproducible Discovery Rate (IDR)
  • 2bedGraphToBigWig
  • 2bedToBigBed
  • 2cutadapt
  • 2deepTools
  • 2fastp
  • 2overlap_peaks.py
  • 2sambamba
  • 1Phantompeakqualtools
  • 1Trim Galore
  • 1getVariantOverlap.py
  • 1makeCandidateRegions.py
  • 1predict.py
  • 1run.neighborhoods.py
Developed by
  • 1AMP-T2D consortium

Showing 1 of 1 results

table-tab-iconmatrix-icon

  • Pipeline

    DPL707AXE

    active

    ATAC-seq Pipeline (ENCODE replicated)
    Assays: ATAC-seq
    Software: Bowtie 2, Samtools, Picard, cutadapt, sambamba, overlap_peaks.py, bedToBigBed, Irreproducible Discovery Rate (IDR), BEDTools, MACS2, Phantompeakqualtools
  • Contact
  • Terms of Use
  • AMP Consortium sign-in

©2025 Regents of the University of California.

  • UC San Diego