IGVFFI9112WEDK

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI9112WEDK/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI9112WEDK",
10    "aliases": [
11        "ansuman-satpathy:igvf17_peaks_10x3"
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": "56d4a6cec8123c5492b71a0c8012b87b",
26    "content_type": "peaks",
27    "controlled_access": false,
28    "creation_timestamp": "2025-01-28T06:32:45.775086+00:00",
29    "derived_from": [
30        "/tabular-files/IGVFFI8360SRWO/"
31    ],
32    "file_format": "bed",
33    "file_format_specifications": [
34        {
35            "@id": "/documents/07404908-2ed4-4286-8345-97e0fc205b36/",
36            "description": "10X Genomics Peaks Bedfile"
37        }
38    ],
39    "file_format_type": "bed3",
40    "file_set": {
41        "@id": "/analysis-sets/IGVFDS3457PPSX/",
42        "@type": [
43            "AnalysisSet",
44            "FileSet",
45            "Item"
46        ],
47        "accession": "IGVFDS3457PPSX",
48        "controlled_access": false,
49        "data_use_limitation_summaries": [
50            "No limitations"
51        ],
52        "file_set_type": "intermediate analysis",
53        "samples": [
54            {
55                "@id": "/multiplexed-samples/IGVFSM6345RLEH/",
56                "@type": [
57                    "MultiplexedSample",
58                    "Sample",
59                    "Item"
60                ],
61                "accession": "IGVFSM6345RLEH",
62                "classifications": [
63                    "differentiated cell specimen",
64                    "multiplexed sample"
65                ],
66                "disease_terms": [],
67                "modifications": [],
68                "sample_terms": [
69                    {
70                        "@id": "/sample-terms/EFO_0009320/",
71                        "status": "released",
72                        "term_name": "RUES2"
73                    }
74                ],
75                "status": "released",
76                "summary": "multiplexed sample: Homo sapiens (female) RUES2 differentiated cell specimen induced to gastrula for 2 days; Homo sapiens (female) RUES2 differentiated cell specimen induced to gastrula for 1 day; ... and 10 more samples",
77                "taxa": "Homo sapiens",
78                "treatments": []
79            }
80        ],
81        "status": "released",
82        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
83    },
84    "file_size": 3182619,
85    "gene_list_for": [],
86    "href": "/tabular-files/IGVFFI9112WEDK/@@download/IGVFFI9112WEDK.bed.gz",
87    "input_file_for": [],
88    "integrated_in": [],
89    "lab": {
90        "@id": "/labs/ansuman-satpathy/",
91        "title": "Ansuman Satpathy, Stanford"
92    },
93    "loci_list_for": [],
94    "md5sum": "8d0dd5e4f2e876a3a1ea4d1505c4d4fc",
95    "primer_design_for": [],
96    "quality_metrics": [],
97    "release_timestamp": "2025-03-07T06:05:29.632179+00:00",
98    "s3_uri": "s3://igvf-files/2025/01/28/c6ee4504-97a9-48cf-bd5d-c2882b756e34/IGVFFI9112WEDK.bed.gz",
99    "schema_version": "15",
100    "status": "released",
101    "submitted_by": {
102        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
103        "title": "Christopher Mcginnis"
104    },
105    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l3_peaks.bed",
106    "summary": "GRCh38 peaks",
107    "upload_status": "validation exempted",
108    "uuid": "c6ee4504-97a9-48cf-bd5d-c2882b756e34",
109    "validation_error_detail": "{\"md5sum\": \"original md5sum 56d4a6cec8123c5492b71a0c8012b87b does not match newly calculated md5sum 8d0dd5e4f2e876a3a1ea4d1505c4d4fc.\", \"validate_files\": \"Error [file=/home/ubuntu/igvf-files/2025/01/28/c6ee4504-97a9-48cf-bd5d-c2882b756e34/IGVFFI9112WEDK.bed.gz, line=390147]: chrom KI270727.1 not found [KI270727.1\\t52069\\t52944]\\nAborting ... found error.\"}",
110    "workflow": {
111        "@id": "/workflows/IGVFWF1453HVEC/",
112        "name": "Satpathy Cell Ranger",
113        "uniform_pipeline": false
114    }
115}