Quaich config used for MCM paper bulk Hi-C data analsyis

quaich_config.yaml

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

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

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
saddle:
    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
insulation:
    do: True
    resolution_limits:
        - 10000
        - 50000
    windows:
        - 200000
        - 500000
        - 1000000
    strength_threshold: 0.1
    fold_change_threshold: 5
    chunksize: 1000000000
    max_tad_length: 1500000

call_dots:
    do: True
    resolution: 5000
    samples:
        - Unsynchronized
        - Untagged_AtAFB2
        - MCM2-AID_+Aux
        - MCM2-AID_-Aux_87322
        - MCM2-AID_+Aux_87320

bed_pairs:
    path: /exports/igmm/eddie/wendy-lab/ilia/MCM/beds/bed_pairs/
    input:
        convergent_CTCF:
            arguments: ""
            files:
                - CTCF_MCM2AID_DMSO_pos.bed
                - CTCF_MCM2AID_DMSO_neg.bed

compare_boundaries_samples:
    - Unsynchronized
    - Unsynchronized_Auxin360mins

call_TADs_samples:
    - Unsynchronized