Example config file for quaich

quaich_example_config.yaml

genome: hg38
path_genomes: /exports/igmm/eddie/wendy-lab/ilia/genomes/

project_folder: /exports/igmm/eddie/wendy-lab/ilia/quaich_example/

filter: mapq_30

resolutions:
    - 10000000
    - 5000000
    - 2500000
    - 1000000
    - 500000
    - 250000
    - 100000
    - 50000
    - 25000
    - 10000
    - 5000
    - 2000
    - 1000

ignore_resolutions_more_than: 1000000
eigenvector:
    do: True
    resolution_limits:
        - 50000
        - 250000

saddles:
    do: True
    bins:
        - 10
        - 25
        - 50
        - 100
    distance_limits:
        - 1600000
        - 102400000
    args: --strength --quantiles --qrange 0.01 0.99

pileups:
    do: True
    resolution_limits:
        - 1000
        - 5000
    distance_limits:
        - 12500
        - 102400000
    shifts: 1
    rescale_pad: 1
    bed_pairs:
        path: /exports/igmm/eddie/wendy-lab/ilia/quaich_example/beds/bedpairs/
        input:
            convergent_CTCF:
                arguments: ""
                files:
                    - CTCF_MCM2AID_DMSO_pos.bed
                    - CTCF_MCM2AID_DMSO_neg.bed
insulation:
    do: True
    resolution_limits:
        - 10000
        - 50000
    windows:
        - 200000
        - 500000
        - 1000000
    strength_threshold: 0.1
    fold_change_threshold: 5
    chunksize: 1000000000

call_dots:
    do: True
    resolution: 5000
    samples:
        - Unsynchronized
        - Unsynchronized_Auxin360mins

compare_boundaries:
    do: True
    samples:
        - Unsynchronized
        - Unsynchronized_Auxin360mins

call_TADs:
    do: True
    max_tad_length: 1500000
    samples:
        - Unsynchronized