IGVFFI3542THRK

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI3542THRK/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI3542THRK",
10    "aliases": [
11        "ansuman-satpathy:igvf13_peaks_10x2"
12    ],
13    "analysis_step_version": "/analysis-step-versions/699d6738-4033-4afc-b6f3-1d82a80e0b41/",
14    "assay_titles": [
15        "10x multiome with MULTI-seq"
16    ],
17    "assembly": "GRCh38",
18    "audit": {},
19    "award": {
20        "@id": "/awards/HG011972/",
21        "component": "functional characterization"
22    },
23    "barcode_map_for": [],
24    "checkfiles_version": "v14",
25    "content_md5sum": "a66279ea146af2fc79f46db3bf31c69e",
26    "content_type": "peaks",
27    "controlled_access": true,
28    "creation_timestamp": "2025-01-28T06:24:49.882850+00:00",
29    "derived_from": [
30        "/tabular-files/IGVFFI9484EEZH/"
31    ],
32    "file_format": "bed",
33    "file_format_specifications": [
34        "/documents/07404908-2ed4-4286-8345-97e0fc205b36/"
35    ],
36    "file_format_type": "bed3",
37    "file_set": {
38        "@id": "/analysis-sets/IGVFDS0226SGHL/",
39        "@type": [
40            "AnalysisSet",
41            "FileSet",
42            "Item"
43        ],
44        "accession": "IGVFDS0226SGHL",
45        "file_set_type": "intermediate analysis",
46        "samples": [
47            {
48                "@id": "/multiplexed-samples/IGVFSM7106DAZZ/",
49                "@type": [
50                    "MultiplexedSample",
51                    "Sample",
52                    "Item"
53                ],
54                "accession": "IGVFSM7106DAZZ",
55                "classifications": [
56                    "tissue",
57                    "multiplexed sample"
58                ],
59                "disease_terms": [
60                    {
61                        "@id": "/phenotype-terms/MONDO_0005010/",
62                        "@type": [
63                            "PhenotypeTerm",
64                            "OntologyTerm",
65                            "Item"
66                        ],
67                        "status": "released",
68                        "summary": "coronary artery disorder",
69                        "term_name": "coronary artery disorder"
70                    }
71                ],
72                "modifications": [],
73                "sample_terms": [
74                    {
75                        "@id": "/sample-terms/UBERON_0001626/",
76                        "status": "released",
77                        "term_name": "left coronary artery"
78                    }
79                ],
80                "status": "released",
81                "summary": "multiplexed sample: Homo sapiens (female, 48 years) left coronary artery tissue associated with coronary artery disorder; Homo sapiens (female, 73 years) left coronary artery tissue associated with coronary artery disorder; ... and 2 more samples",
82                "taxa": "Homo sapiens",
83                "treatments": []
84            }
85        ],
86        "status": "released",
87        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq): cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
88    },
89    "file_size": 726502,
90    "gene_list_for": [],
91    "href": "/tabular-files/IGVFFI3542THRK/@@download/IGVFFI3542THRK.bed.gz",
92    "input_file_for": [],
93    "integrated_in": [],
94    "lab": {
95        "@id": "/labs/ansuman-satpathy/",
96        "title": "Ansuman Satpathy, Stanford"
97    },
98    "loci_list_for": [],
99    "md5sum": "5e224ea03ba149348a1a300bfec09c73",
100    "primer_design_for": [],
101    "quality_metrics": [],
102    "release_timestamp": "2025-03-22T00:43:55.011605+00:00",
103    "s3_uri": "s3://igvf-restricted-files/2025/01/28/ca6f0917-7e4d-4155-8a6c-3a47befbc5c6/IGVFFI3542THRK.bed.gz",
104    "schema_version": "15",
105    "status": "released",
106    "submitted_by": {
107        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
108        "title": "Christopher Mcginnis"
109    },
110    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l2_peaks.bed",
111    "summary": "GRCh38 peaks",
112    "upload_status": "validation exempted",
113    "uuid": "ca6f0917-7e4d-4155-8a6c-3a47befbc5c6",
114    "validation_error_detail": "{\"md5sum\": \"original md5sum a66279ea146af2fc79f46db3bf31c69e does not match newly calculated md5sum 5e224ea03ba149348a1a300bfec09c73.\", \"validate_files\": \"Error [file=/home/ubuntu/igvf-restricted-files/2025/01/28/ca6f0917-7e4d-4155-8a6c-3a47befbc5c6/IGVFFI3542THRK.bed.gz, line=85908]: chrom KI270728.1 not found [KI270728.1\\t232215\\t233180]\\nAborting ... found error.\"}",
115    "workflow": {
116        "@id": "/workflows/IGVFWF1453HVEC/",
117        "name": "Satpathy Cell Ranger",
118        "uniform_pipeline": false
119    }
120}