Histone_ChIP-seq_ENCSR000DUF
Histone_ChIP-seq ENCSR000DUF [biosample_summary="Homo sapiens HepG2" and target="H3K4me3"]
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| Id: | Histone_ChIP-seq/ENCSR000DUF |
| Type: | position_score |
| Version: | 0 |
| Summary: |
HistoneChIP-seq ENCSR000DUF [biosamplesummary="Homo sapiens HepG2" and target="H3K4me3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN264CHY|/analyses/ENCAN264CHY/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF663ZBD|/files/ENCFF663ZBD/} processed by ChIP-seq ENCODE3 hg19 pipeline has 11307693 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 {ENCFF053ZWM|/files/ENCFF053ZWM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 11534142 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 {ENCFF663ZBD|/files/ENCFF663ZBD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF663ZBD|/files/ENCFF663ZBD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.25. 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 {ENCFF053ZWM|/files/ENCFF053ZWM/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF053ZWM|/files/ENCFF053ZWM/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.59. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DUF | float |
Histone_ChIP-seq_ENCSR000DUF |
Histone_ChIP-seq ENCSR000DUF [biosample_summary="Homo sapiens HepG2" and target="H3K4me3"]
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[1.83, 114] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF712HMU.bed.gz | 923.63 KB | 716624a776f9f6d22890dec6ba2f4798 |
| ENCFF712HMU.bed.gz.dvc | 100.0 B | d82e2de1e2839bde7ea880a1bc9fd1e5 |
| ENCFF712HMU.tabix.bed.gz | 398.4 KB | 747276115c8b3c3dba05412f48675d31 |
| ENCFF712HMU.tabix.bed.gz.dvc | 106.0 B | 77d99639c667d82ce9b6ceda9f678467 |
| ENCFF712HMU.tabix.bed.gz.tbi | 160.46 KB | 6c84d570c21080b5077ceac33be9bae4 |
| ENCFF712HMU.tabix.bed.gz.tbi.dvc | 110.0 B | 3928413bfe3d8409fd6a0c6e4ab6ae25 |
| genomic_resource.yaml | 4.95 KB | 66c4ab4bc4347c52968cad058172997b |
| genomic_resource_original.yaml | 4.84 KB | e98897aa7321c3e34837a04f26105501 |
| statistics/ |