This is the Docker version of Juicer.
Juicer is a platform for analyzing kilobase resolution Hi-C data. For general questions, please use
the Google Group.
If you use Juicer in your research, please cite: Neva C. Durand, Muhammad S. Shamim, Ido Machol, Suhas S. P. Rao, Miriam H. Huntley, Eric S. Lander, and Erez Lieberman Aiden. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments." Cell Systems 3(1), 2016.
- Install Docker
- Download test fastq files:
cd /path/to/testdir
wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R1_001.fastq.gz
wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/work/HIC003/fastq/HIC003_S2_L001_R2_001.fastq.gz
- Put the fastqs in a folder titled
fastq:
mkdir fastq
mv HIC003*.fastq.gz fastq
- Type
docker run aidenlab/juicer:latestAfter downloading the image, the usage message should appear. - Have your reference and restriction site file available under a directory (here juicedir)
- Run Juicer on the test set via
docker run -v /path/to/testdir:/data -v /path/to/juicedir:/juicedir aidenlab/juicer:latest -d /data -z /juicedir/references/Homo_sapiens_assembly19.fasta -y /juicedir/restriction_sites/hg19_MboI.txt -p hg19 -s MboI
The parameter -v /path/to/testdir:/data mounts your directory as /data in the Docker image.
Everything after aidenlab/juicer:latest is a command to Juicer, not a Docker command. So the parameter -d /data tells
Juicer that your files live at the mount point /data. The results of the Juicer run will be written out to this directory;
you will see directories aligned and splits created underneath your test directory /path/to/testdir
The parameters -z /juicedir/references/Homo_sapiens_assembly19.fasta and -y /juicedir/restriction_sites/hg19_MboI.txt tell Juicer
where to look for your reference file/bwa index files and your restriction site file. The parameter -p hg19 gives the genome ID or
alternatively, location of the chrom.sizes file.
You can call Juicer with all of the usual flags. For instance, to include fragment maps, use the -f flag. To change the number of threads used by BWA, use the -t flag. To ignore any restriction site information, use -s none.
Please see the Juicer documentation for extensive usage information.
The test set above is the HIC003 fastqs from Rao & Huntley et al. | Cell 2014. A larger test set, consisting of chromosome 19 from the combined GM12878 map from that paper, is available below. This test set will produce domains (and theoretically loops, though HiCCUPS requires GPUs and Docker does not support them).
wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/work/MBR19/fastq/chr19_R1.fastq.gz
wget https://s3.amazonaws.com/juicerawsmirror/opt/juicer/work/MBR19/fastq/chr19_R2.fastq.gz
On a Mac, you might have to change your preferences to add memory for BWA.
Click the Docker whale to edit your Preferences. Then edit your memory and CPUs in the Advanced tab.
