FAN-C command line tools

The fanc tool should be accessible from the command line after you installed FAN-C (see Installation). It provides convenient commands for the generation, modification, and analysis of Hi-C data.

• Overview and shared parameters
  • Overview
  • Logging
  • Email notifications
  • Temporary files
  • FAN-C config files
• Working with Cooler, Juicer, and text files
  • Cooler .cool and .mcool
  • Juicer .hic files
  • Text files
• Generate Hi-C matrices
  • fanc auto: Automated generation of Hi-C matrices
  • Individual pipeline steps
  • Helper tools
  • Configuration options
• Analyse Hi-C matrices
  • Expected values and O/E matrices
  • AB compartments
  • PCA
  • TADs and TAD boundaries
  • Matrix and score comparisons
  • Aggregate Hi-C matrices
  • Loop calling