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 $ juicer.sh -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 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
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.