• ATAC-seq pipeline
• General
• Details
  • Pre-analysis
    • pre-QC:
    • trim:
    • alignment:
    • post processing:
    • shift reads:
    • post qc:
    • generate summary metrics:
  • Core analysis
    • peak calling:
  • Advanced analysis
    • peak anno and comparison:
    • Diff peak analysis:
    • motif scan:
    • footprint:

ATAC-seq pipeline

General

Refer to this review paper: Yan, F., Powell, D.R., Curtis, D.J. et al. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis. Genome Biol 21, 22 (2020). https://doi.org/10.1186/s13059-020-1929-3

Also the ENCODE specification here.

Details

1&2: Pre-analysis

1A: Pre-QC:

fastqc

1B: Trim:

trimmomatic

1C: Post-QC

fastqc

2A: Index Genome

bwa index

2B: Alignment:

bwa mem

2C: Filter and calculate PBC:

picard MarkDuplicates picard CollectAlignmentSummaryMetrics picard CollectInsertSizeMetrics

samtools MT removal, low quality removal, unmapped/unpaired/not proper paired removal % mapped, % chrM, % dup, % after all filtering PBC1, PBC2, and NRF

2D: Shift reads:

perl scripts

Core analysis

3: peak calling:

macs2 shift and extend mode, narrowpeak with summit, broad mode HMMRATAC

Advanced analysis

peak anno and comparison:

upsetplot, ChIPseeker

Diff peak analysis:

motif scan:

FIMO, Homer

footprint:

HINT-ATAC