Juicer is a one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can:
Go from raw fastq files to Hi-C maps binned at many resolutions Automatically annotate loops and contact domains with the Juicer tools Run the pipeline in the cloud, on LSF, Univa, or SLURM, or on a single CPU
Juicer creates hic files from raw (unaligned) reads derived from a Hi-C experiment.
The BioGrids version of juicer renames the main juicer.sh script to include the run type: juicer_cpu.sh juicer_aws.sh juicer_slurm.sh juicer_lsf.sh juicer_uger.sh
To use any of these, first link the juicer files to your current run directory, as shown in the documentation. For example, with a CPU run:
For Linux: ln -s /programs/x86_64-linux/juicer/1.5.6/CPU/scripts ./
For Mac: ln -s /programs/i386-mac/juicer/1.5.6/CPU/scripts ./
Then run the renamed juicer script from your run directory: time juicer_cpu.sh -D /build/source/juicer/1.5.6
N. C. Durand, M. S. Shamim, Machol I, S. S. Rao, M. H. Huntley, E. S. Lander, and A. EL.. 2016. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 3(1): 95-98.
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