export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a; module load java; export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/juicer_tools.1.8.9/; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2019/2019-08-05-NextSeq-run/juicer-L856-Apo-on_beads_PCR -d /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2019/2019-08-05-NextSeq-run/juicer-L856-Apo-on_beads_PCR -p /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.1/GCA_001417965.1_Aiptasia_genome_1.1_genomic.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.1/bwa-indexes/Aiptasia_pallida-1.1_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.1/bwa-indexes/GCA_001417965.1_Aiptasia_genome_1.1_genomic.fa