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This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication.  The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler.  We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "display_title": "4DNFII7498B3.mcool", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFII7498B3/@@download/4DNFII7498B3.mcool", "file_format": {"display_title": "mcool", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "file_format": "mcool", "@id": "/file-formats/mcool/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@id": "/higlass-view-configs/6ea80421-c098-4856-8de3-52fe7e062bfb/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFII7498B3 - contact matrix for GM12878 Dilution Hi-C HindIII", "uuid": "6ea80421-c098-4856-8de3-52fe7e062bfb", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "Dilution Hi-C", "experiment_bucket": "Results of 4DN DCIC HiC Pipeline, early version", "assay_info": "HindIII", "dataset": "Hi-C on GM12878 cells - protocol variations", "condition": "Selvaraj et al Nature Biotech 2013", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for GM12878 Dilution Hi-C HindIII"}, "quality_metric": {"status": "released", "@id": "/quality-metrics-mcool/5ade92b0-cec0-4401-9713-1c501c6094d4/", "display_title": "QualityMetricMcool from 2021-05-21", "overall_quality_status": "PASS", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "uuid": "5ade92b0-cec0-4401-9713-1c501c6094d4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "last_modified": {"date_modified": "2023-08-25T17:56:46.690062+00:00"}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f108ebb3-8693-491a-88a0-d3e2163d9966/4DNFIDWULZXP.normvector.juicerformat.gz", "status": "released", "file_size": 7482067, "uuid": "f108ebb3-8693-491a-88a0-d3e2163d9966", "file_type_detailed": "juicebox norm vector (normvector_juicerformat)", "accession": "4DNFIDWULZXP", "@id": "/files-processed/4DNFIDWULZXP/", "file_type": "juicebox norm vector", "genome_assembly": "GRCh38", "display_title": "4DNFIDWULZXP.normvector.juicerformat.gz", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFIDWULZXP/@@download/4DNFIDWULZXP.normvector.juicerformat.gz", "file_format": {"display_title": "normvector_juicerformat", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f226118b2c", "file_format": "normvector_juicerformat", "@id": "/file-formats/normvector_juicerformat/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "Dilution Hi-C", "experiment_bucket": "Results of 4DN DCIC HiC Pipeline, early version", "assay_info": "HindIII", "dataset": "Hi-C on GM12878 cells - protocol variations", "condition": "Selvaraj et al Nature Biotech 2013", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2022-01-10T18:00:44.019228+00:00"}}], "title": "Results of 4DN DCIC HiC Pipeline, early version", "description": "Moved from archived_processed_files "}], "@id": "/experiments-hi-c/4DNEXBZAHAQZ/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "ecc8555e-1eda-4c07-85a6-642322ad3577", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Dilution Hi-C on GM12878 with HindIII - 4DNEXBZAHAQZ", "external_references": [{"ref": "SRA:SRX318776", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX318776"}], "experiment_sets": [{"experimentset_type": "replicate", "display_title": "4DNESLLTENG9", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESLLTENG9", "uuid": "10d1c941-87af-44d9-ac29-8bdcb15d4ca7", "@id": "/experiment-set-replicates/4DNESLLTENG9/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"@type": ["Publication", "Item"], "ID": "PMID:24185094", "date_published": "2013-12-09", "abstract": "Rapid advances in high-throughput sequencing facilitate variant discovery and genotyping, but linking variants into a single haplotype remains challenging. Here we demonstrate HaploSeq, an approach for assembling chromosome-scale haplotypes by exploiting the existence of 'chromosome territories'. We use proximity ligation and sequencing to show that alleles on homologous chromosomes  occupy distinct territories, and therefore this experimental protocol preferentially recovers physically linked DNA variants on a homolog. Computational analysis of such data sets allows for accurate ( approximately 99.5%) reconstruction of chromosome-spanning haplotypes for approximately 95% of  alleles in hybrid mouse cells with 30x sequencing coverage. To resolve haplotypes for a human genome, which has a low density of variants, we coupled HaploSeq with local conditional phasing to obtain haplotypes for approximately 81% of alleles with approximately 98% accuracy from just 17x sequencing. Whereas methods based on proximity ligation were originally designed to investigate spatial organization of genomes, our results lend support for their use as a general tool for haplotyping.", "title": "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.", "short_attribution": "Selvaraj S et al. (2013)", "status": "current", "authors": ["Selvaraj S", "R Dixon J", "Bansal V", "Ren B"], "uuid": "088313f3-b588-4b71-8372-e202ba3baa97", "display_title": "Selvaraj S et al. 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We use proximity ligation and sequencing to show that alleles on homologous chromosomes  occupy distinct territories, and therefore this experimental protocol preferentially recovers physically linked DNA variants on a homolog. Computational analysis of such data sets allows for accurate ( approximately 99.5%) reconstruction of chromosome-spanning haplotypes for approximately 95% of  alleles in hybrid mouse cells with 30x sequencing coverage. To resolve haplotypes for a human genome, which has a low density of variants, we coupled HaploSeq with local conditional phasing to obtain haplotypes for approximately 81% of alleles with approximately 98% accuracy from just 17x sequencing. 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