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dLEM

dLEM: differentiable Loop Extrusion Model

Usage:

$ dlem [OPTIONS] DNA_INTS OUTPUT_LOCATION

Arguments:

  • DNA_INTS: Chromatin input dataset in the form of a .cool file [required]
  • OUTPUT_LOCATION: Location of output directory, will be created if not existing [required]

Options:

  • --device [gpu|cpu|tpu]: Select computation device. [default: cpu]
  • -r, --region TEXT: Print details about a specific target chromosomal region (ex: chr16:51906425-55560999), this includes plotting and track output. By default dLEM learns the whole chromosome (ex: chr16) the target region lies in.
  • -b, --bed TEXT: Define target regions in BED file to plot and output tracks for, Plot and output tsv for all regions in BED file, 3 columns , ex: .
  • --chromosomes COMMA_LIST_PARSER: Comma-separated list of chromosomes to train dLEM on (e.g., 'chr1,chr2,chr3').
  • --all: Run dLEM across all chromosomes in input chromatin loop file.
  • -l, --resolution INTEGER: Resolution to pull .cool file from .mcool file, must exist.
  • --start-diag INTEGER: Diagonal offset where updates start during training. [default: 5]
  • --train-rows INTEGER: Number of diagonals to use during training dLEM. [default: 170]
  • --steps INTEGER: Number of steps for training. [default: 10]
  • -w, --window-size INTEGER: Column window size for slowdown fitting [default: 3000]
  • -s, --window-step INTEGER: Step between slowdown-fitting windows. [default: 200]
  • -d, --decay-extent INTEGER: Number of band rows to use when fitting slowdown. [default: 500]
  • -i, --iterations INTEGER: Number of iterations to fit the model over. [default: 300]
  • -lr, --lr FLOAT: Change speed of parameter tuning, useful if loss is too fast/slow or model not converging. [default: 0.01]
  • -pm, --prediction-mode [mse|corr|final]: Which parameter set to use for predictions. [default: mse]
  • -pr, --prediction-rows INTEGER: Number of diagonals to predict when outputting dLEM predictions [default: 700]
  • --full-output: Predict all diagonals in output instead of a set number
  • -esm, --early-stop-metric [mse|corr|none]: Metric for early stopping [default: mse]
  • --debug: Verbose output during training
  • -c, --output-cool: Output the prediction as a .cool file
  • -t, --output-tracks: Output the parameters as genomic tracks for target regions in BED and whole genome in BigWig format
  • --norm: Normalize the predicted band using geometric mean
  • -p, --plot: Plot fits to compare to input
  • --install-completion: Install completion for the current shell.
  • --show-completion: Show completion for the current shell, to copy it or customize the installation.
  • --help: Show this message and exit.