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Juicer

What is Juicer?

Juicer is a one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can

• Go from raw fastq files to Hi-C maps binned at many resolutions
• Automatically annotate loops and contact domains with the Juicer tools
• Run the pipeline in the cloud, on LSF, Univa, or SLURM, or on a single CPU

Juicer creates hic files from raw (unaligned) reads derived from a Hi-C experiment.

Juicer Tools Pre creates hic files from aligned Hi-C reads (i.e., lists of Hi-C contacts).

Follow the links below to get started:

• Installation
  • Dependencies
  • Directory Structure
• Running Juicer
• Detailed usage