{"lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "title": "4DN DCIC, HMS", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Pairs are merged and aggregated with `pairix` version 0.3.3. Pairs files are then converted to `mcool` via `cooler` version 0.8.5.\n\nMerging:\n\n* There is no merging of sequencing replicates. Processing is performed separately for each sequencing replicate.\n* Biological replicates are merged using the same method as used by the Hi-C processing pipeline. That is,\n * Biological replicates are merged after the duplicate removal step, since PCR duplication events happen independently in each replicate.\n * Merging is performed on `pairs` files using [run-merge-pairs.sh](https://github.com/4dn-dcic/docker-4dn-hic/blob/master/scripts/run-merge-pairs.sh).\n * 4DN DCIC provides a merged output as a merged `pairs` file.\n\nFile Format Conversion:\n\n* `mcool` files are contact matrices containing multiple resolutions which can be visualized in [HiGlass](http://higlass.io/).\n* The 4DN standard resolutions for `mcool` files are: 1kb, 2kb, 5kb, 10kb, 25kb, 50kb, 100kb, 250kb, 500kb, 1Mb, 2.5Mb, 5Mb, 10Mb.\n\nSource files (v1.1.1\\_dcic\\_4):\n\n* Workflow: https://data.4dnucleome.org/workflows/4DNWFMRGIPC1/\n* CWL: https://github.com/4dn-dcic/iMARGI-Docker/blob/v1.1.1_dcic_4/src/cwl/imargi-processing-pairs.cwl\n* Docker (for merging only): https://github.com/4dn-dcic/docker-4dn-hic/tree/v43", "name": "resources.data-analysis.imargi-processing-pipeline.aggregation", "award": {"@type": ["Award", "Item"], "@id": "/awards/2U01CA200059-06/", "status": "current", "project": "4DN", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "name": "2U01CA200059-06", "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, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "center_title": "DCIC - Park", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Aggregation", "status": "released", "aliases": ["4dn-dcic-lab:resources.data-analysis.imargi-processing-pipeline.aggregation"], "options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "date_created": "2021-10-04T15:29:54.387430+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-03-26T18:53:39.345240+00:00"}, "schema_version": "2", "@id": "/static-sections/e504cbe6-5440-4c5b-8ecb-3d40bd2d8ff8/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "e504cbe6-5440-4c5b-8ecb-3d40bd2d8ff8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.545f1931-792c-4a7e-83b3-3e91baea4e30"]}, "display_title": "Aggregation", "external_references": [], "content": "Pairs are merged and aggregated with `pairix` version 0.3.3. Pairs files are then converted to `mcool` via `cooler` version 0.8.5.\n\nMerging:\n\n* There is no merging of sequencing replicates. Processing is performed separately for each sequencing replicate.\n* Biological replicates are merged using the same method as used by the Hi-C processing pipeline. That is,\n * Biological replicates are merged after the duplicate removal step, since PCR duplication events happen independently in each replicate.\n * Merging is performed on `pairs` files using [run-merge-pairs.sh](https://github.com/4dn-dcic/docker-4dn-hic/blob/master/scripts/run-merge-pairs.sh).\n * 4DN DCIC provides a merged output as a merged `pairs` file.\n\nFile Format Conversion:\n\n* `mcool` files are contact matrices containing multiple resolutions which can be visualized in [HiGlass](http://higlass.io/).\n* The 4DN standard resolutions for `mcool` files are: 1kb, 2kb, 5kb, 10kb, 25kb, 50kb, 100kb, 250kb, 500kb, 1Mb, 2.5Mb, 5Mb, 10Mb.\n\nSource files (v1.1.1\\_dcic\\_4):\n\n* Workflow: https://data.4dnucleome.org/workflows/4DNWFMRGIPC1/\n* CWL: https://github.com/4dn-dcic/iMARGI-Docker/blob/v1.1.1_dcic_4/src/cwl/imargi-processing-pairs.cwl\n* Docker (for merging only): https://github.com/4dn-dcic/docker-4dn-hic/tree/v43", "filetype": "md", "content_as_html": "

Pairs are merged and aggregated with pairix version 0.3.3. Pairs files are then converted to mcool via cooler version 0.8.5.

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Merging:

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File Format Conversion:

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Source files (v1.1.1_dcic_4):

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