Generate Hi-C matrices

• fanc auto: Automated generation of Hi-C matrices
  • Parameters
  • Input types
  • Test runs and Sun/Oracle/Slurm Grid engine support
  • Next steps
• Individual pipeline steps
  • fanc map: Mapping FASTQ files
  • fanc pairs: Generating and filtering read Pairs
  • fanc hic: Generating, binning, and filtering Hic objects
• Helper tools
  • fanc from-txt: import Hic from text file
  • fanc dump: export Hic objects to text file
  • fanc subset: create Hic objects by subsetting
  • fanc downsample: downsample Hic objects
  • fanc fragments: in silico genome digestion
  • fanc sort-sam: sort SAM files by name
• Configuration options