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Installation
- The latest version of GNU CoreUtils
- The latest version of the Burrows-Wheeler Aligner (BWA)
- You must install CUDA for HiCCUPS peak calling, and use an NVIDIA GPU.
- The native libraries included with Juicer are compiled for CUDA 7. Other versions of CUDA can be used, but you will need to download the respective native libraries from JCuda.
- For best performance, use a dedicated GPU. You may also be able to obtain access to GPU clusters through Amazon Web Services or a local research institution.
- You must install the Java 1.7 or 1.8 JDK. (Alternative link for Ubuntu/LinuxMint)
Juicer requires the use of a cluster, with ideally >= 4 cores (min 1 core) and >= 64 GB RAM (min 16 GB RAM). Juicer currently works with the following resource management software:
Make sure to copy the appropriate scripts from the github repo to your cluster as well as the fastq reads and appropriate reference files.
The following shows a sample configuration of the all the files and directories on the cluster once Juicer is fully set up (using AWS as an example). It assumes that all files needed by Juicer are set up under /opt/juicer. You can also access a public mirror of these files by going to https://s3.amazonaws.com/juicerawsmirror/opt/juicer/[paths_below], for example: https://s3.amazonaws.com/juicerawsmirror/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R1_001.fastq.gz.
# tmp directory
/opt/juicer/tmp
# sample work directory is /opt/juicer/work/HIC003
/opt/juicer/work/HIC003/fastq
/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R1_001.fastq.gz
/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R2_001.fastq.gz
# another sample work directory is /opt/juicer/work/MBR19
/opt/juicer/work/MBR19/fastq
/opt/juicer/work/MBR19/fastq/chr19_R1.fastq.gz
/opt/juicer/work/MBR19/fastq/chr19_R2.fastq.gz
# Core Juicer scripts from github in /opt/juicer/scripts
/opt/juicer/scripts/chimeric_blacklist.awk
/opt/juicer/scripts/statistics.pl
/opt/juicer/scripts/stats_sub.awk
/opt/juicer/scripts/split_rmdups.awk
/opt/juicer/scripts/countligations.sh
/opt/juicer/scripts/juicebox
/opt/juicer/scripts/juicebox_tools.jar
/opt/juicer/scripts/juicer_postprocessing.sh
/opt/juicer/scripts/dups.awk
/opt/juicer/scripts/juicer.sh
/opt/juicer/scripts/LibraryComplexity.class
/opt/juicer/scripts/hicInternalMenu.properties
/opt/juicer/scripts/abnormal.awk
/opt/juicer/scripts/check.sh
/opt/juicer/scripts/fragment.pl
/opt/juicer/scripts/makemega_addstats.awk
/opt/juicer/scripts/mega.sh
/opt/juicer/scripts/relaunch_prep.sh
/opt/juicer/scripts/cleanup.sh
# Sequence reference files in /opt/juicer/references
# hg19 and mm9 reference files in mirror
/opt/juicer/references/Homo_sapiens_assembly19.fasta
/opt/juicer/references/Mus_musculus_assembly9_norandom.fasta
Make sure to copy the appropriate scripts from the github repo to your cluster as well as the fastq reads and appropriate reference files.
After running BWA indexing (might take a couple hours) bwa index <fasta file>:
# after running BWA indexing
/opt/juicer/references/Homo_sapiens_assembly19.fasta.sa
/opt/juicer/references/Homo_sapiens_assembly19.fasta.ann
/opt/juicer/references/Homo_sapiens_assembly19.fasta.amb
/opt/juicer/references/Homo_sapiens_assembly19.fasta.pac
/opt/juicer/references/Homo_sapiens_assembly19.fasta.bwt
/opt/juicer/references/Mus_musculus_assembly9_norandom.fasta.bwt
/opt/juicer/references/Mus_musculus_assembly9_norandom.fasta.amb
/opt/juicer/references/Mus_musculus_assembly9_norandom.fasta.pac
/opt/juicer/references/Mus_musculus_assembly9_norandom.fasta.ann
/opt/juicer/references/Mus_musculus_assembly9_norandom.fasta.sa
After building the restriction sites files python generate_site_positions.py <enzyme> <genome ID> <fasta>
https://github.com/theaidenlab/juicer/blob/master/misc/generate_site_positions.py
# restriction sites files in /opt/juicer/restriction_sites
/opt/juicer/restriction_sites/mm9_HindIII.txt
/opt/juicer/restriction_sites/mm10_MboI.txt
/opt/juicer/restriction_sites/mm10_DpnII.txt
/opt/juicer/restriction_sites/hg19_MboI.txt
/opt/juicer/restriction_sites/hg38_MboI.txt
/opt/juicer/restriction_sites/hg38_DpnII.txt
/opt/juicer/restriction_sites/hg19_DpnII.txt
/opt/juicer/restriction_sites/hg19_HindIII_new.txt
/opt/juicer/restriction_sites/mm9_DpnII.txt