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-L1027-Tetrahymena_thermophila_Hi-C_MluCl -d /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2019/2019-09-16-NextSeq-run/juicer-L1027-Tetrahymena_thermophila_Hi-C_MluCl -p /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bwa-indexes/Tetrahymena_thermophila_MluCl.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bwa-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.fa