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
  • 1ATAC-seq
Pipeline status
  • 1active
Pipeline groups
  • 1ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
Software
  • 17Samtools
  • 15MACS2
  • 14BEDTools
  • 13Bowtie 2
  • 12Picard
  • 8bedGraphToBigWig
  • 8bedToBigBed
  • 8cutadapt
  • 7sambamba
  • 6STAR
  • 5RSEM
  • 5overlap_peaks.py
  • 4BWA
  • 4Irreproducible Discovery Rate (IDR)
  • 4deepTools
  • 4fastp
  • 4ptools_bin
  • 3Phantompeakqualtools
  • 2Concat-fastq
  • 2Median Absolute Deviation
  • 2RNA pipelines
  • 2TopHat
  • 2lrna-index-rsem
  • 2lrna-index-star
  • 2lrna-index-tophat
  • 2lrna-mad-qc
  • 2lrna-quantification
  • 2lrna-signals
  • 1Association testing and fine mapping: eQTL-Catalogue/qtlmap
  • 1BEDOPS
  • 1ChromHMM
  • 1CoLo
  • 1Digital genomic footprinting
  • 1Gene expression QC and normalisation: eQTL-Catalogue/qcnorm
  • 1Genotype QC and imputation: eQTL-Catalogue/genimpute
  • 1RNA-seq quantification: eQTL-Catalogue/rnaseq
  • 1SALMON
  • 1SRA_Toolkit
  • 1Tophat BAM Repair
  • 1Trim Galore
  • 1getVariantOverlap.py
  • 1hotspot2
  • 1lrna-align-star-pe
  • 1lrna-align-star-se
  • 1lrna-align-tophat-pe
  • 1lrna-align-tophat-se
  • 1lrna-signals-stranded
  • 1lrna-signals-unstranded
  • 1makeCandidateRegions.py
  • 1predict.py
  • 1run.neighborhoods.py
  • 1unknown
Developed by
  • 1Kyle Gaulton, UCSD

Showing 1 of 1 results

table-tab-iconmatrix-icon

  • Pipeline

    DPL961ZQY

    active

    ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
    Assays: ATAC-seq
    Software: Trim Galore, BWA, Samtools, Picard, MACS2
  • Contact
  • Terms of Use
  • AMP Consortium sign-in

©2024 Regents of the University of California.

  • UC San Diego