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@Phlya
Created September 11, 2020 15:28
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Quaich config used for MCM paper bulk Hi-C data analsyis
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
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