Histone_ChIP-seq_ENCSR000DVN
Histone_ChIP-seq ENCSR000DVN [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K4me3"]
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| Id: | Histone_ChIP-seq/ENCSR000DVN |
| Type: | position_score |
| Version: | 0 |
| Summary: |
HistoneChIP-seq ENCSR000DVN [biosamplesummary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K4me3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: newborn output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN684XIM|/analyses/ENCAN684XIM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF288CHB|/files/ENCFF288CHB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10738235 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed alignments file {ENCFF841TST|/files/ENCFF841TST/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15521940 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF841TST|/files/ENCFF841TST/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF841TST|/files/ENCFF841TST/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.07. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DVN | float |
Histone_ChIP-seq_ENCSR000DVN |
Histone_ChIP-seq ENCSR000DVN [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K4me3"]
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[2.01, 106] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF657MIQ.bed.gz | 632.34 KB | 9e55ae38241a1fcfa1f6e75776fcd482 |
| ENCFF657MIQ.bed.gz.dvc | 100.0 B | 8ee78988060dd3ac6aaf1a0d7b8e992c |
| ENCFF657MIQ.tabix.bed.gz | 267.69 KB | 955b1d7a74a64923c5fa11016346beea |
| ENCFF657MIQ.tabix.bed.gz.dvc | 106.0 B | cfc1a0225ca6b6baf2a0db1e354a8364 |
| ENCFF657MIQ.tabix.bed.gz.tbi | 137.23 KB | 5726c9584edb8bafec403a4fea3cb969 |
| ENCFF657MIQ.tabix.bed.gz.tbi.dvc | 110.0 B | d4338d82e8e1f63c2bca3f8703b46e50 |
| genomic_resource.yaml | 4.15 KB | 2511dcd56afc1ca639e4c6c4b5b0fb11 |
| genomic_resource_original.yaml | 4.01 KB | b5aef75cc2f44b226f13efc37f4ee990 |
| statistics/ |