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/2019/2019-09-16-NextSeq-run/juicer-L1029-Cyanophora_paradoxa_Hi-C -d /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2019/2019-09-16-NextSeq-run/juicer-L1029-Cyanophora_paradoxa_Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Glaucophyta/Cyanophora_paradoxa-Cyanophora_CLC_112010/Cyanophora_CLC_112010.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Glaucophyta/Cyanophora_paradoxa-Cyanophora_CLC_112010/bwa-indexes/Cyanophora_paradoxa-Cyanophora_CLC_112010_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Glaucophyta/Cyanophora_paradoxa-Cyanophora_CLC_112010/bwa-indexes/Cyanophora_CLC_112010.fa