TF_ChIP-seq_ENCSR000ALV
TF_ChIP-seq ENCSR000ALV [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="CTCF"]
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| Id: | TF_ChIP-seq/ENCSR000ALV |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000ALV [biosamplesummary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="CTCF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (50 years) output_type: IDR thresholded peaks audit_error: Processed alignments file {ENCFF472NHA|/files/ENCFF472NHA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 4916002 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-human and investigated as a transcription factor 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_internal_action: Released analysis {ENCAN429XCN|/analyses/ENCAN429XCN/} has in progress subobject document {52887bb2-dff6-4639-93be-2be188fc853c|/documents/52887bb2-dff6-4639-93be-2be188fc853c/} audit_internal_action: Released analysis {ENCAN429XCN|/analyses/ENCAN429XCN/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF086QJQ|/files/ENCFF086QJQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 9512981 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-human and investigated as a transcription factor 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 {ENCFF086QJQ|/files/ENCFF086QJQ/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF086QJQ|/files/ENCFF086QJQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.35. 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 {ENCFF472NHA|/files/ENCFF472NHA/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF472NHA|/files/ENCFF472NHA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.76. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000ALV | float |
TF_ChIP-seq_ENCSR000ALV |
TF_ChIP-seq ENCSR000ALV [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="CTCF"]
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[2.33, 230] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF059YXD.bed.gz | 607.33 KB | 4203b524c4826e167130c1d0f0482a05 |
| ENCFF059YXD.bed.gz.dvc | 100.0 B | 826216450d5fb39ef144617e0ea2eb63 |
| ENCFF059YXD.tabix.bed.gz | 465.72 KB | e78486a0283671e2ea21dd61dc919800 |
| ENCFF059YXD.tabix.bed.gz.dvc | 106.0 B | c313bc1d1486ff5bd9735d5053b2e0b0 |
| ENCFF059YXD.tabix.bed.gz.tbi | 266.68 KB | 0f05c143204181d998dcf53fa223ac1c |
| ENCFF059YXD.tabix.bed.gz.tbi.dvc | 110.0 B | 717b51e8611932ea1b7cc3ab9579a215 |
| genomic_resource.yaml | 5.25 KB | 93e0e411a76be1ec78f4284a06f8ba09 |
| genomic_resource_original.yaml | 5.11 KB | 55e026869a98523aaea9a175da9c7316 |
| statistics/ |