juicer¶

Description¶

Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps.

Environment Modules¶

Run module spider juicer to find out what environment modules are available for this application.

Environment Variables¶

HPC_JUICER_DIR - installation directory
HPC_JUICER_BIN - executable directory

Additional Usage Information¶

The juicer pipeline creates a series of batch jobs and submits them all at once using job dependencies.

We provide four variants of the main script with different resource options:

juicer.sh -- submit all jobs to investment qos of user's default (primary) account.
juicer-b.sh -- same as juicer.sh; additionally submit alignment jobs to the burst qos of user's primary account.
juicer_2ndgrp.sh -- submit all jobs to an account specified with the -A option. Facilitates use of secondary account resources.
juicer_2ndgrp-b.sh -- same as juicer_2ndgrp.sh; additionally submit alignment jobs to the burst qos of specified account.

Type "juicer.sh -h" to see options and help menu.

Template script¶

juicer job scripts need to be run on the command line on a login node - not submitted with sbatch as a slurm job!

$ ml juicer
$ juicer_2ndgrp-b.sh \
-d /blue/group/$USER/juicer \
-A "group" \
-C 40000000 \
-z $HPC_JUICER_REFS/hg38.fa \
-y $HPC_JUICER_SITES/hg38_Arima.txt \
-p $HPC_JUICER_SITES/hg38.chrom.sizes \

Juicer depends on reference files (bwa index plus chromosome sizes file) and restriction enzyme files that are part of the central install. See $HPC_JUICER_DIR/references and $HPC_JUICER_DIR/restriction_sites for available reference data. Users can build additional references in under their accounts, or ask UFRC staff to generate them centrally.

Categories¶

genomics