Hich documentation

• Install Hich and its dependencies
  • Download the Hich pipeline
  • Create the hich environment and install dependencies
• Configuration
  • Sample file
  • Params file
  • Nextflow config file
  • Set samples at the command line
  • Set Hich-config at the command line
  • Hich-config reference
    • Typically specified in params file
      • Analysis methods and analysis plans
    • Typically specified in nextflow.config
  • Sample attributes reference
    • Relationships between samples
    • Resource files
    • Aligning reads
    • Filters
    • Hi-C contacts ingested from .pairs or parsed from .sam/.bam
    • Filtering Hi-C contacts
    • Downsampling, merging, and deduplicating samples
    • Creating contact matrices
    • Generating multiQC reports on Hi-C contacts
    • Sample selection strategies
    • Calling HiCRep SCC scores
    • Calling compartment scores
    • Calling insulation scores
    • Calling loops
    • Calling differential loop enrichments (diffloops)
    • Recent outputs
    • Hich sample attributes built automatically (not typically manually specified by user)
• Hich CLI Utilities
  • hich compartments [options] REFERENCE MATRIX RESOLUTION
  • hich digest [options] REFERENCE DIGEST
  • hich downsample [options] INPUT_PAIRS_PATH OUTPUT_PAIRS_PATH
  • hich fragtag [options] FRAGFILE OUT_PAIRS IN_PAIRS
  • hich gather [options]
  • hich hicrep [options] PATHS
  • hich reshape [options]
  • hich stats_aggregate [options] STATS-PATHS
  • hich stats [options]
• Vignettes
• Workflow Steps
• Planning The Workflow
• Implementation