Histone_ChIP-seq_ENCSR000DQM
Histone_ChIP-seq ENCSR000DQM [biosample_summary="Homo sapiens Caco-2" and target="H3K4me3"]
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| Id: | Histone_ChIP-seq/ENCSR000DQM |
| Type: | position_score |
| Version: | 0 |
| Summary: |
HistoneChIP-seq ENCSR000DQM [biosamplesummary="Homo sapiens Caco-2" and target="H3K4me3"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN478IKG|/analyses/ENCAN478IKG/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF448CAQ|/files/ENCFF448CAQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 11036240 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 {ENCFF069VSC|/files/ENCFF069VSC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 11447300 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 {ENCFF448CAQ|/files/ENCFF448CAQ/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF448CAQ|/files/ENCFF448CAQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.59. 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 {ENCFF069VSC|/files/ENCFF069VSC/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF069VSC|/files/ENCFF069VSC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.29. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DQM | float |
Histone_ChIP-seq_ENCSR000DQM |
Histone_ChIP-seq ENCSR000DQM [biosample_summary="Homo sapiens Caco-2" and target="H3K4me3"]
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[1.95, 114] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF434CLI.bed.gz | 737.25 KB | 89edb9db5a7c2bdc6473ed0dc62b13c1 |
| ENCFF434CLI.bed.gz.dvc | 100.0 B | 0abed3470f9c6fb21b4318abe1e8923a |
| ENCFF434CLI.tabix.bed.gz | 313.24 KB | 158ada4e7ace70861b9b77d19123e7b4 |
| ENCFF434CLI.tabix.bed.gz.dvc | 106.0 B | 9f3ada5937352e31bffa45606b5eb05c |
| ENCFF434CLI.tabix.bed.gz.tbi | 144.38 KB | 1c81b0b8e7c451ee4d4474f1b06ab4db |
| ENCFF434CLI.tabix.bed.gz.tbi.dvc | 110.0 B | 800d700f4dbf1d8b09121e8562204d8a |
| genomic_resource.yaml | 5.26 KB | ae7460cd59d965ecfb494551fff74c6e |
| genomic_resource_original.yaml | 5.15 KB | f301f7e2c3d8f8e5f85dbf8a5fef6923 |
| statistics/ |