Histone_ChIP-seq_ENCSR000DUO
Histone_ChIP-seq ENCSR000DUO [biosample_summary="Homo sapiens HL-60" and target="H3K4me3"]
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| Id: | Histone_ChIP-seq/ENCSR000DUO |
| Type: | position_score |
| Version: | 0 |
| Summary: |
HistoneChIP-seq ENCSR000DUO [biosamplesummary="Homo sapiens HL-60" and target="H3K4me3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN506YWM|/analyses/ENCAN506YWM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF693QTE|/files/ENCFF693QTE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 7623406 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_not_compliant: Processed alignments file {ENCFF355WJQ|/files/ENCFF355WJQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9161715 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 {ENCFF693QTE|/files/ENCFF693QTE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF693QTE|/files/ENCFF693QTE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.95. 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 {ENCFF355WJQ|/files/ENCFF355WJQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF355WJQ|/files/ENCFF355WJQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.20. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DUO | float |
Histone_ChIP-seq_ENCSR000DUO |
Histone_ChIP-seq ENCSR000DUO [biosample_summary="Homo sapiens HL-60" and target="H3K4me3"]
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[2.09, 184] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF034USW.bed.gz | 665.25 KB | 488ff0debfd714b9b780ad391b56e9d9 |
| ENCFF034USW.bed.gz.dvc | 100.0 B | 5848b9898004568f93a928aa942cf329 |
| ENCFF034USW.tabix.bed.gz | 284.28 KB | 16af41c3dbe669b545a33b9363e3130d |
| ENCFF034USW.tabix.bed.gz.dvc | 106.0 B | a330e47446a144354c9345afd138ce12 |
| ENCFF034USW.tabix.bed.gz.tbi | 135.56 KB | e2ba29d8ec437ea80b51b4145a6ca65c |
| ENCFF034USW.tabix.bed.gz.tbi.dvc | 110.0 B | 5cf11523e4c655472d4e812d28daea4c |
| genomic_resource.yaml | 5.27 KB | 4462263a44e0b23fbc0e30ff44a2e858 |
| genomic_resource_original.yaml | 5.16 KB | 7fcd7ac822a6d672cc25dc8e86664681 |
| statistics/ |