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config.yaml
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config.yaml
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#####
# Spectral clustering parameters
#####
params:
# Resolution of contact map to use.
binsize: 50000
# Total number of eigenvectors to compute.
n_eigs: 128
# Number of clusters K for K-means runs.
n_clusters: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 32, 64]
# Decomposition mode: trans or cis (beta)
decomp_mode: 'trans'
#####
# Genome and Hi-C data
#####
assembly:
name: hg38
fasta_path: ../resources/hg38.fa
samples:
# Unique sample name
H9:
# Path to an mcool file
cooler_path: ../resources/4DNFIT5YVTLO.mcool
# Path to a BED3 file marking interchromosomal translocations and other
# trans artifacts that interfere with clustering.
blacklist_path: ../resources/h9.blacklist.bed
#####
# Track configuration
#####
# List of binned quantitative genomic tracks to use for visualization of
# eigenspace and clustering.
# Each track has a type:
# * category: categorical data
# * scalar: quantitative
# * divergent: quantitative, but the default colorscale will be centered at 0.
# Colormapping options for matplotlib/datashader can be specified.
# Each track type has associated default options which can be overridden.
tracks:
# These are some of the default tracks generated during the pipeline.
cluster:
type: "category"
chrom:
type: "category"
GC:
type: "divergent"
options:
cmap: "RdYlBu_r"
vmin: 0.35
vmax: 0.65
centel_abs:
type: "scalar"
options:
cmap: "Greys"
vmin: 0
vmax: 149043529
# Specify additional tracks to be generated from bigwig files.
# Their display options can be customized here.
# Default is to assume type: "scalar".
H2AK5ac:
type: "scalar"
H2BK12ac:
type: "scalar"
H2BK15ac:
type: "scalar"
# Metadata file specifying additional bigwig tracks. See README.
# The aggregated tracks will be stored in an HDF5 file.
bigwig_metadata_path: ../config/track_metadata.tsv
#####
# Configure which tracks to use in each visualization.
#####
heatmap_groups:
group1:
- centel_abs
- GC
group2:
- H2AK5ac
- H2BK12ac
- H2BK15ac
scatter_groups:
group1:
- cluster
- centel_abs
- GC
- H2AK5ac
- H2BK12ac
- H2BK15ac