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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.



See which versions of juicer are available:

$ module avail juicer

Load one version into your environment and run it:

$ module load juicer/1.6
$ -h


Testing juicer with the included sample data:

$ module load juicer/1.6
$ mkdir -p 2021-01-18-juicer/fastq
$ cd 2021-01-18-juicer/fastq
$ wget
$ cd -
$ -d ~/2021-01-18-juicer


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ tar xf 1.6.tar.gz
$ cd juicer-1.6
$ mkdir references; cd references
$ wget \ \ \ \ \
$ mkdir ../restriction_sites; cd ../restriction_sites
$ wget
$ cd ..
$ ln -s SLURM/scripts .
$ cd scripts
$ wget
$ ln -s juicer_tools.1.9.9_jcuda.0.8.jar juicer_tools.jar
$ cd ..
$ sed -i -e '/sbatch_mem_alloc/d' -e '/--mem/d' scripts/
# edit for HPC hostname stuff
$ sudo mkdir -p /export/apps/juicer/1.6
$ sudo cp -r * /export/apps/juicer/1.6

Note 1: There are several modifications we need to do to get to run on our cluster. First, the addition of a check to see if it is running at ILRI versus Aiden lab, and second to remove the SBATCH memory options because we don't use those on our cluster.

juicer-software.txt · Last modified: 2021/01/19 07:54 by aorth