Juicer installation

This is an instruction of Juicer installation for CPU version, which can deal with Hi-C data.

Create and conda environment for Juicer:

conda create –name juicer
conda activate juicer

Download the Juicer and reference files:

mkdir ~/opt/Juicer
git clone https://github.com/theaidenlab/juicer.git
cd ~/opt/Juicer
ln -s ~/juicer/CPU scripts
cd scripts/common
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 ../..

Blow is just an example for Juicer data format, please see the Juicer build below

mkdir references
cp <my_reference_fastas_and_indices> references/

# this is optional, only needed for fragment-delimited files

ln -s <myRestrictionSiteDir> restriction_sites
cd <myWorkingDir>
mkdir fastq
mv <fastq_files> fastq/
~/opt/Juicer/scripts/juicer.sh -D <myJuicerDir>

Installation the dependencies for Juicer:

1) GNU CoreUtils conda install -c conda-forge coreutils 2) Burrows-Wheeler Aligner (BWA) conda install -c bioconda bwa

Build the Juicer using reference data

1) Make the reference folder mkdir juicer_data cd juicer_data mkdir references; cd references wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.amb wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.ann wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.bwt wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.pac wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/references/Homo_sapiens_assembly19.fasta.sa cd ..

2) Build the restriction site folder mkdir restriction_sites; cd restriction_sites wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/restriction_sites/hg19_MboI.txt awk ‘BEGIN{OFS=”\t”}{print $1, $NF}’ hg19_MboI.txt > hg19.chrom.sizes cd ..

3) Build the dataset from Hi-C mkdir HIC003; cd HIC003 mkdir fastq; cd fastq wget http://juicerawsmirror.s3.amazonaws.com/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R1_001.fastq.gz wget http://juicerawsmirror.s3.amazonaws.com/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R2_001.fastq.gz cd ..