Histone_ChIP-seq_ENCSR000DUQ
Histone_ChIP-seq ENCSR000DUQ [biosample_summary="Homo sapiens mammary epithelial cell female" and target="H3K4me3"]
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| Id: | Histone_ChIP-seq/ENCSR000DUQ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
HistoneChIP-seq ENCSR000DUQ [biosamplesummary="Homo sapiens mammary epithelial cell female" and target="H3K4me3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: female output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN687DIN|/analyses/ENCAN687DIN/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF029KZM|/files/ENCFF029KZM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13184720 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 {ENCFF995CUR|/files/ENCFF995CUR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17156259 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 {ENCFF029KZM|/files/ENCFF029KZM/} 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 {ENCFF029KZM|/files/ENCFF029KZM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.29. 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 {ENCFF995CUR|/files/ENCFF995CUR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF995CUR|/files/ENCFF995CUR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.40. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DUQ | float |
Histone_ChIP-seq_ENCSR000DUQ |
Histone_ChIP-seq ENCSR000DUQ [biosample_summary="Homo sapiens mammary epithelial cell female" and target="H3K4me3"]
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[2.04, 117] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF296VDQ.bed.gz | 807.8 KB | d05fa830d1e1656170e919b36e6366de |
| ENCFF296VDQ.bed.gz.dvc | 100.0 B | dbe3dcee0731eeedbeb1de11347e90a9 |
| ENCFF296VDQ.tabix.bed.gz | 350.49 KB | adcad9ca0b221056515d47d8e21ad67d |
| ENCFF296VDQ.tabix.bed.gz.dvc | 106.0 B | d55d3a685025dfe56120182d31143cfd |
| ENCFF296VDQ.tabix.bed.gz.tbi | 155.79 KB | da3b633c5229ccb239e59ce84fafa342 |
| ENCFF296VDQ.tabix.bed.gz.tbi.dvc | 110.0 B | 19262a57345fec1229bfe8ba2173a76e |
| genomic_resource.yaml | 5.1 KB | b2d9dd32217fd8637f5a895f7ef8f120 |
| genomic_resource_original.yaml | 4.98 KB | 5c5b38a4727679d43c64bd8b66265d93 |
| statistics/ |