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Parameters for the Modules

The dcHiChIP pipeline provides flexible module-level control through a comprehensive set of parameters. Below is an overview of key parameters categorized by module, with default values and usage notes.

Mandatory Input Paramters

  • max_cpus: Maximum Allocated CPU
  • max_memory: Maximum Allocated Memory
  • max_time: Maximum Execution Time
  • input: Location of the samplesheet
  • fasta: Location of the bwa index file
  • genomics_features: Location of the genomic fetures
  • outdir: Location of the output directory
  • genome_size: reference genome (eg, hs or mm)

Other Parameters

bwa mem

  • mapq: MAPping Quality (Phred-scaled)
  • -t: Number of threads

samtools

  • --threads: Number of threads

MACS3

  • --qvalue: q-value (minimum FDR) cutoff to call significant regions [Default = 0.05]

MAPS

  • bin_size: resolution. Usually 5000 or 10000. [Default = 5000]
  • binning_range: How far 3D interactions can be called, also affects the estimate of the expected count. [Default=1000000]
  • sex_chroms_to_process: either X,Y,XY or NA. [Default = NA]
    • This specifies which (if any) sex chromosomes the user wants to run MAPS on: X = X chr only, Y = Y chr only, XY = both X and Y chroms, NA = none (just autosomal).

DeepTools (plotCoverage, multiBigwigSummary)

  • --numberOfProcessors: Number of processors to use [Default = 1]
  • --binSize: Size (in bases) of the windows sampled from the genome. [Default: 10000]

HOMER(findMotifsGenome.pl)

  • -p: Number of CPUs to use [Default 1]
  • -S: Number of motifs to find [Default 25)

Stripe Calling (gStripe)

  • --max_workers: Number of CPUs to use [Default 1]

Open2C (pairtools)

  • --nproc: Number of processes

Open2C (cooler Zomify)

  • --nproc: Number of processes to use for batch processing chunks of pixels [Default: 1]
  • --resolutions: Comma-separated list of target resolutions.
    • Use suffixes B or N to specify a progression:
    • B for binary (geometric steps of factor 2)
    • N for nice (geometric steps of factor 10 interleaved with steps of 2 and 5)
      • Examples:
        • 1000B → 1000, 2000, 4000, 8000, …
        • 1000N → 1000, 2000, 5000, 10000, …
        • 5000N → 5000, 10000, 25000, 50000, …

Open2C (cooltools insulation)

  • --nproc: Number of processes to split the work between. [Default: 1]
  • <res>: resolution [Default: 1000 2000 5000 10000 20000 50000 100000 200000 500000]

Open2C (cooltools insulation)

  • --nproc: Number of processes to split the work between. [Default: 1]
  • <res>: resolution [Default: 100000]

CALDER

  • --ncores: Number of processes to split the work between. [Default: 1]
  • <res>: resolution [Default: 100000]

3Dmodelling (MultiMM)

  • --platform: name of the platform. Available choices: CPU, OpenCL, CUDA. [Default: CPU]
  • --cpu_threads: Number of CPU threads (in case that CPU is chosen as platform).
  • --modelling_level: Helping function to specify parameters of simulation.
    • Choose ‘GENE’, ‘REGION’, ‘CHROM’, or ‘GW’ depending on the resolution of interest.
  • --gene_name: The name of the gene of interest. {Only valid when –modelling_level = GENE}
  • --chrom: Chromosome that corresponds the the modelling region of interest
    • case-sensivite for chr21 (not accepted : CHR21, Chr21, 21) {Only valid when –modelling_level = REGION/CHROM }
  • --loc_start: Starting region coordinate {Only valid when –modelling_level = REGION}
  • --loc_end: Ending region coordinate {Only valid when –modelling_level = REGION}