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.

• Version: 1.6
• Added: January, 2021
• Link: https://github.com/aidenlab/juicer

See which versions of juicer are available:

$ module avail juicer

Load one version into your environment and run it:

$ module load juicer/1.6
$ juicer.sh -h

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/aidenlab/juicer/archive/1.6.tar.gz
$ tar xf 1.6.tar.gz
$ cd juicer-1.6
$ mkdir references; cd references
$ wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.amb \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.ann \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.bwt \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.pac \
     https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.sa
$ mkdir ../restriction_sites; cd ../restriction_sites
$ wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/restriction_sites/hg19_MboI.txt
$ cd ..
$ ln -s SLURM/scripts .
$ cd scripts
$ wget https://hicfiles.tc4ga.com/public/juicer/juicer_tools.1.9.9_jcuda.0.8.jar
$ 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/juicer.sh
# edit juicer.sh 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 juicer.sh 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.

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 http://juicerawsmirror.s3.amazonaws.com/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R1_001.fastq.gz http://juicerawsmirror.s3.amazonaws.com/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R2_001.fastq.gz
$ cd -
$ juicer.sh -d ~/2021-01-18-juicer