project:
  assay: bulk_ATAC_seq
  comparison: Memory_NK_relative_to_Mature_NK
  genome_build: GRCh38
  release_snapshot: 2026-08-28

compute:
  maximum_total_threads: 2
  concurrent_intensive_processes: 1

week1_training:
  sample_id: SRR7650763
  cell_type: Immature_NK
  treatment: untreated
  scope: chromosome_22_teaching_subset
  included_in_final_comparison: false
  alignment_minimum_mapq: 30
  blacklist_removal: pair_preserving
  peak_caller: MACS3_3.0.2
  peak_format: BAMPE
  peak_qvalue: 0.05

week2_consensus_and_counts:
  mature_samples: 4
  memory_samples: 6
  condition_union_merge_distance: 0
  consensus_regions: 112759
  count_unit: paired_fragments
  featurecounts_version: 2.1.1
  featurecounts_options: "-F SAF -p --countReadPairs -B -C -s 0 -T 2"

primary_differential_analysis:
  minimum_count: 10
  minimum_samples: 5
  total_samples: 10
  tested_regions: 59186
  design: "~ donor + cell_type"
  reference_level: Mature_NK
  contrast: Memory_NK_relative_to_Mature_NK
  adjusted_pvalue_threshold: 0.05
  absolute_log2_fold_change_threshold: 1
  shrinkage: apeglm
  significant_dars_ordinary_lfc: 0
  significant_dars_apeglm_lfc: 0

exploratory_followup:
  nominal_raw_pvalue_threshold: 0.05
  strict_nominal_set:
    definition: "raw p < 0.05 and absolute apeglm LFC >= 1 under the primary 10-in-5 filter"
    regions: 21
    memory_direction: 11
    mature_direction: 10
  annotation: GENCODE_release_50_GRCh38_primary_assembly
  homer_target_regions: 1562
  homer_background_regions: 59186
  homer_window_bp: 200
  interpretation: exploratory_only_not_fdr_significant