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ATAC Sequencing

Domain key: atacseq

ATAC-seq maps open chromatin regions genome-wide using Tn5 transposase. The Tn5 insertion bias requires a read-shift correction step that Codaris applies automatically before peak calling.

Step Tool Notes
QC FastQC Pre-alignment quality check
Trimming TrimGalore Adapter trimming
Alignment Bowtie2 --very-sensitive preset
BAM filtering SAMtools / Picard Remove MT reads, duplicates
Peak calling MACS2 BAMPE mode for paired-end
ATAC QC ataqv TSS enrichment, fragment size

Best Practices Enforced

  • Bowtie2 is always run with --very-sensitive for ATAC-seq sensitivity
  • Mitochondrial reads (chrM) are filtered out before any downstream analysis
  • Reads are shifted +4 bp (forward) and −5 bp (reverse) to account for Tn5 transposase offset
  • MACS2 is called in --format BAMPE mode for paired-end libraries
  • ataqv is run to report TSS enrichment score — values below 7 are flagged as QC failures

Example Prompts

Build an ATAC-seq pipeline for mouse samples aligned to mm10.
I need peak calls and TSS enrichment QC. Paired-end reads.

codaris > ATAC-seq — I have bulk frozen PBMC samples, 150bp PE reads.
          Make sure chrM is removed and the Tn5 shift is applied.

codaris > My ATAC-seq TSS enrichment is 4.2. Check the pipeline —
          is the read shifting and chrM filter applied correctly?