IGVFFI6324ICSV

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI6324ICSV/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
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9    "accession": "IGVFFI6324ICSV",
10    "aliases": [
11        "ansuman-satpathy:igvf16_peaks_10x5"
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": "9b6b388b6541db052e6f237c48b688d1",
26    "content_type": "peaks",
27    "controlled_access": true,
28    "creation_timestamp": "2025-02-14T22:55:03.759461+00:00",
29    "derived_from": [
30        "/tabular-files/IGVFFI2494BZRQ/"
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/IGVFDS4086WMME/",
39        "@type": [
40            "AnalysisSet",
41            "FileSet",
42            "Item"
43        ],
44        "accession": "IGVFDS4086WMME",
45        "file_set_type": "intermediate analysis",
46        "samples": [
47            {
48                "@id": "/multiplexed-samples/IGVFSM1943HMCZ/",
49                "@type": [
50                    "MultiplexedSample",
51                    "Sample",
52                    "Item"
53                ],
54                "accession": "IGVFSM1943HMCZ",
55                "classifications": [
56                    "differentiated cell specimen",
57                    "multiplexed sample"
58                ],
59                "disease_terms": [],
60                "modifications": [],
61                "sample_terms": [
62                    {
63                        "@id": "/sample-terms/EFO_0004905/",
64                        "status": "released",
65                        "term_name": "induced pluripotent stem cell"
66                    }
67                ],
68                "status": "released",
69                "summary": "multiplexed sample: Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 11 days; Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 3 days; ... and 6 more samples",
70                "taxa": "Homo sapiens",
71                "treatments": []
72            }
73        ],
74        "status": "released",
75        "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
76    },
77    "file_size": 2787591,
78    "gene_list_for": [],
79    "href": "/tabular-files/IGVFFI6324ICSV/@@download/IGVFFI6324ICSV.bed.gz",
80    "input_file_for": [],
81    "integrated_in": [],
82    "lab": {
83        "@id": "/labs/ansuman-satpathy/",
84        "title": "Ansuman Satpathy, Stanford"
85    },
86    "loci_list_for": [],
87    "md5sum": "fc185b4d60d8b8b5189fc29d7533e43d",
88    "notes": "Lab did not use official IGVF consortium selected genome. Checkfiles could not recognize: KI270728.1. Therefore, validation is exempted",
89    "quality_metrics": [],
90    "release_timestamp": "2025-03-22T00:44:41.248487+00:00",
91    "s3_uri": "s3://igvf-restricted-files/2025/02/14/37d77363-7629-48ba-ad81-a893f5cc57cf/IGVFFI6324ICSV.bed.gz",
92    "schema_version": "15",
93    "status": "released",
94    "submitted_by": {
95        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
96        "title": "Christopher Mcginnis"
97    },
98    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf16/e16l5_peaks.bed.gz",
99    "summary": "GRCh38 peaks",
100    "upload_status": "validation exempted",
101    "uuid": "37d77363-7629-48ba-ad81-a893f5cc57cf",
102    "validation_error_detail": "{\"validate_files\": \"Error [file=/home/ubuntu/igvf-restricted-files/2025/02/14/37d77363-7629-48ba-ad81-a893f5cc57cf/IGVFFI6324ICSV.bed.gz, line=340199]: chrom KI270728.1 not found [KI270728.1\\t232276\\t233171]\\nAborting ... found error.\"}",
103    "workflow": {
104        "@id": "/workflows/IGVFWF1453HVEC/",
105        "name": "Satpathy Cell Ranger",
106        "uniform_pipeline": false
107    }
108}