{"lab": {"correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "#### What is the difference between Juicer and Cooler?\nJuicer 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`.\n\n#### How do I run the Hi-C pipeline on my own data?\nThe 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).\n\nAlternatively, 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\n\n#### How do I run the Hi-C pipeline without Docker support?\nThe 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.\n\nAfter installing the required software, one can run the actual commands as in https://github.com/4dn-dcic/docker-4dn-hic/blob/master/HiCPipeline.md\n\n#### Do you have a TAD caller?\nNo, we currently do not have a TAD caller.\n", "name": "resources.data-analysis.hi_c-processing-pipeline.faq", "award": {"name": "1U01CA200059-01", "center_title": "DCIC - DCIC", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "project": "4DN", "@type": ["Award", "Item"], "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators with a strong track record in analysis of chromatin interaction data, image processing and three-dimensional data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and flexible cloud technologies. In Aim 1, we will develop efficient submission pipelines for data and metadata from 4DN data production groups. We will define data/metadata requirements and quality metrics in conjunction with the production groups and ensure that high-quality, well- annotated data become available to the wider scientific community in a timely manner. In Aim 2, we will develop a user-friendly data portal for the broad scientific community. This portal will provide an easy-to-navigate interface for accessing raw and intermediate data files, allow for programmatic access via APIs, and will incorporate novel analysis and visualization tools developed by DCIC as well as other Network members. For computing and storage scalability and cost-effectiveness, significant efforts will be devoted to development and deployment of cloud-based technology. We will conduct tutorials and workshops to facilitate the use of 4DN data and tools by external investigators. In Aim 3, we will coordinate and assist in conducting integrative analysis of the multiple data types. These efforts will examine key questions in higher-order chromatin organization using both sequence and image data, and the tools and algorithms developed here will be incorporated into the data portal for use by other investigators. These three aims will ensure that the data generated in 4DN will have maximal impact for the scientific community.", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Hi-C pipeline", "status": "released", "aliases": ["4dn-dcic-lab:resources.data-analysis.hi_c-processing-pipeline.faq"], "options": {"filetype": "md", "collapsible": true, "default_open": true}, "date_created": "2020-04-22T20:33:37.391612+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-03-23T20:15:35.181333+00:00"}, "schema_version": "2", "@id": "/static-sections/a74c30a4-d577-4934-b1d1-a39091a29eee/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "a74c30a4-d577-4934-b1d1-a39091a29eee", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267998888"]}, "display_title": "Hi-C pipeline", "external_references": [], "content": "#### What is the difference between Juicer and Cooler?\nJuicer 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`.\n\n#### How do I run the Hi-C pipeline on my own data?\nThe 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).\n\nAlternatively, 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\n\n#### How do I run the Hi-C pipeline without Docker support?\nThe 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.\n\nAfter installing the required software, one can run the actual commands as in https://github.com/4dn-dcic/docker-4dn-hic/blob/master/HiCPipeline.md\n\n#### Do you have a TAD caller?\nNo, we currently do not have a TAD caller.\n", "filetype": "md", "content_as_html": "

What is the difference between Juicer and Cooler?

\n

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.

\n

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

\n

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).

\n

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

\n

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

\n

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.

\n

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

\n

Do you have a TAD caller?

\n

No, we currently do not have a TAD caller.

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