oracle-chip-seq/config.yaml at main · challagandla/oracle-chip-seq · GitHub

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species: human

references:
  human:
    genome: "/path/to/hg38.fa"
    chrom_sizes: "/path/to/hg38.chrom.sizes"
    black_list: "/path/to/hg38-blacklist.v2.bed"
    bt2_index: "/path/to/hg38"
    name: "hg38"
    gsize: "2.7e9"
    # Example for 150-bp uniquely mapped GRCh38 reads. Recalculate for the
    # assembly, read length, and mapping policy used in the experiment.
    effective_genome_size: 2862010428
  mouse:
    genome: "/path/to/mm39.fa"
    chrom_sizes: "/path/to/mm39.chrom.sizes"
    black_list: "/path/to/mm39-blacklist.v2.bed"
    bt2_index: "/path/to/mm39"
    name: "mm39"
    gsize: "1.87e9"
    # Example for 150-bp uniquely mapped GRCm39 reads.
    effective_genome_size: 2495461690
  rat:
    genome: "/path/to/rn6.fa"
    chrom_sizes: "/path/to/rn6.chrom.sizes"
    black_list: "/path/to/rn6-blacklist.bed"
    bt2_index: "/path/to/rn6"
    name: "rn6"
    gsize: "2.53e9"
    # No universal rn6 value is safe under MAPQ filtering; replace before use.
    effective_genome_size: 0

contamination:
  fastq_screen_conf: "config/fastq_screen.conf"
  subset: 100000

alignment:
  min_mapq: 30
  max_insert_size: 2000

peak_calling:
  narrow_qvalue: 0.01
  broad_cutoff: 0.1
  consensus_min_replicates: 2

differential_binding:
  numerator_condition: treated
  reference_condition: control
  narrow_summits: 200

motif_enrichment:
  window_bp: 200
  background_multiplier: 2
  seed: 1

deeptools:
  threads: 4
  track_bin_size: 25
  matrix_bin_size: 50
  reference_point_upstream: 3000
  reference_point_downstream: 3000
  scale_regions_upstream: 3000
  scale_regions_downstream: 3000
  scale_regions_body_length: 5000
  log2_pseudocount: 1
  log2_scale_method: "None"  # independently CPM-normalize IP and input
  heatmap_color_map: "RdBu_r"
  heatmap_z_min: -2
  heatmap_z_max: 2
  plot_dpi: 200
  # Optional display-only overrides keyed by the original factor name:
  # factor_modes:
  #   H3K27ac: reference_point

chip_controls:
  - id: Input_control_rep1
    condition: control
    fastq:
      - data/raw/Input_control_rep1_R1.fastq.gz
      - data/raw/Input_control_rep1_R2.fastq.gz
  - id: Input_control_rep2
    condition: control
    fastq:
      - data/raw/Input_control_rep2_R1.fastq.gz
      - data/raw/Input_control_rep2_R2.fastq.gz
  - id: Input_treated_rep1
    condition: treated
    fastq:
      - data/raw/Input_treated_rep1_R1.fastq.gz
      - data/raw/Input_treated_rep1_R2.fastq.gz
  - id: Input_treated_rep2
    condition: treated
    fastq:
      - data/raw/Input_treated_rep2_R1.fastq.gz
      - data/raw/Input_treated_rep2_R2.fastq.gz

chip_samples:
  - id: H3K27ac_control_rep1
    fastq:
      - data/raw/H3K27ac_control_rep1_R1.fastq.gz
      - data/raw/H3K27ac_control_rep1_R2.fastq.gz
    control: Input_control_rep1
    condition: control
    replicate: 1
    factor: H3K27ac
    tissue: K562
    peak_mode: narrow  # geometry, not assay class; H3K27ac is punctate
  - id: H3K27ac_control_rep2
    fastq:
      - data/raw/H3K27ac_control_rep2_R1.fastq.gz
      - data/raw/H3K27ac_control_rep2_R2.fastq.gz
    control: Input_control_rep2
    condition: control
    replicate: 2
    factor: H3K27ac
    tissue: K562
    peak_mode: narrow
  - id: H3K27ac_treated_rep1
    fastq:
      - data/raw/H3K27ac_treated_rep1_R1.fastq.gz
      - data/raw/H3K27ac_treated_rep1_R2.fastq.gz
    control: Input_treated_rep1
    condition: treated
    replicate: 1
    factor: H3K27ac
    tissue: K562
    peak_mode: narrow
  - id: H3K27ac_treated_rep2
    fastq:
      - data/raw/H3K27ac_treated_rep2_R1.fastq.gz
      - data/raw/H3K27ac_treated_rep2_R2.fastq.gz
    control: Input_treated_rep2
    condition: treated
    replicate: 2
    factor: H3K27ac
    tissue: K562
    peak_mode: narrow