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juicer

Description

juicer website

Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps.

Environment Modules

Run module spider juicer to find out what environment modules are available for this application.

Environment Variables

  • HPC_JUICER_DIR - installation directory
  • HPC_JUICER_BIN - executable directory

Additional Usage Information

The juicer pipeline submits jobs to the slurm scheduler and then exits. It can therefore be started on a login node. Individual tools (see $HPC_JUICER_DIR/scripts) can be run as batch jobs or interactively.

Type "juicer.sh -h" to see options and help menu.

Juicer depends on reference files (bwa index plus chromosome sizes file) and restriction enzyme files that are part of the central install. See $HPC_JUICER_DIR/references and $HPC_JUICER_DIR/restriction_sites for available reference data. Users can build additional references in under their accounts, or ask UFRC staff to generate them centrally.

Categories

phylogenetics