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 60 -D /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-11-16-NextSeq-run/juicer-L1108-Tetrahymena_starved_Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-11-16-NextSeq-run/juicer-L1108-Tetrahymena_starved_Hi-C -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