{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Micro-C", "status": "released", "cfde_term": {"@id": "/ontology-terms/OBI:0003302/", "display_title": "micro-C assay", "status": "released", "uuid": "816bd12f-df57-465f-9e04-0b6000dc1fdd", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_tags": ["DNA-DNA", "Pairwise", "3D"], "date_created": "2019-03-28T18:53:02.359079+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-03-01T20:39:05.049345+00:00"}, "raw_file_types": "Reads (fastq) provided by lab", "reference_pubs": [{"uuid": "e4e88839-f8e5-4263-93c1-d393c5b10625", "display_title": "Hsieh TH et al. (2015) PMID:26119342", "journal": "Cell", "short_attribution": "Hsieh TH et al. (2015)", "status": "current", "@id": "/publications/e4e88839-f8e5-4263-93c1-d393c5b10625/", "@type": ["Publication", "Item"], "authors": ["Hsieh TH", "Weiner A", "Lajoie B", "Dekker J", "Friedman N", "Rando OJ"], "date_published": "2015-07-02", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "schema_version": "1", "static_content": [{"content": {"content": "The 4DN Hi-C data processing pipeline includes alignment, filtering, and matrix aggregation and normalization steps. Feature calling steps, including insulation scores, compartments, and enriched contacts will be provided in the next version of the pipeline.\n\n
File Type | \nFile Format | \nDescription | \n
---|---|---|
Alignment | \n.bam | \nFiltered alignments of raw reads to the appropriate reference are available in .bam format. These are generated separately for each replicate experiment in an experiment set. | \n
Contact list | \n.pairs | \nContain a list of pairwise contacts and are generated after alignments are filtered. Pairs are generated separately for each replicate, and an additional pairs file is generated after replicates are merged. Quality metrics generated by PairsQC are also provided for each pairs file (a sample report can be found here). | \n
Contact matrix | \n.mcool | \nMulti-resolution contact matrices generated in the final step of the processing pipeline are available in .mcool format, generated by Cooler. These can be visualized on the portal with HiGlass. Mcool contact matrices are normalized with the ICE matrix balancing algorithm (iterative correction and eigenvalue decomposition). | \n
Contact matrix | \n.hic | \nContact matrices generated by Juicertools are also available in .hic format, and these can be visualized externally in Juicebox or in the WashU Epigenome Browser. For in situ Hi-C and dilution Hi-C, the .hic matrix is normalized using the VC, VC_SQRT, KR methods. | \n