StaticSection Hi-C pipeline

What is the difference between Juicer and Cooler?

Juicer is a full Hi-C pipeline, developed at the Lieberman Aiden lab. The 4DN Hi-C pipeline uses juicer_tools pre, a part of Juicer that takes in a pairs file and creates an interaction matrix file in the hic format. Cooler (developed at the Mirny lab at MIT) takes in a pairs file and creates an interaction matrix file in the cool (or mcool) format. The 4DN pipeline also uses Cooler to create an mcool file from the same pairs file used to create a hic file. The hic file can be visualized using Juicebox, whereas the mcool format can be visualized using HiGlass. The hic format is a compressed binary format, whereas cool/mcool formats are based on hdf5.

How do I run the Hi-C pipeline on my own data?

The different steps of the Hi-C pipeline can be run using the CWL files and 4DN Hi-C Docker image, using cwltools (locally) or Tibanna (on the cloud).

Alternatively, one can run the actual commands inside the 4DN Hi-C docker container. The example commands can be found at : https://github.com/4dn-dcic/docker-4dn-hic/blob/master/HiCPipeline.md

How do I run the Hi-C pipeline without Docker support?

The software programs and versions used can be downloaded by running this file https://github.com/4dn-dcic/docker-4dn-hic/blob/master/downloads.sh which was used to create the 4DN Hi-C Docker image.

After installing the required software, one can run the actual commands as in https://github.com/4dn-dcic/docker-4dn-hic/blob/master/HiCPipeline.md

Do you have a TAD caller?

No, we currently do not have a TAD caller.