TF_ChIP-seq_ENCSR000BGS
TF_ChIP-seq ENCSR000BGS [biosample_summary="Homo sapiens GM12878" and target="TAF1"]
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| Id: | TF_ChIP-seq/ENCSR000BGS |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BGS [biosamplesummary="Homo sapiens GM12878" and target="TAF1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN964GJV|/analyses/ENCAN964GJV/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF283MZV|/files/ENCFF283MZV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 12050836 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TAF1-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: Processed alignments file {ENCFF617ZDI|/files/ENCFF617ZDI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 18095793 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TAF1-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 {ENCFF617ZDI|/files/ENCFF617ZDI/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF617ZDI|/files/ENCFF617ZDI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.70. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF502IPK|/files/ENCFF502IPK/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.15 and a self consistency ratio of 2.99. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BGS | float |
TF_ChIP-seq_ENCSR000BGS |
TF_ChIP-seq ENCSR000BGS [biosample_summary="Homo sapiens GM12878" and target="TAF1"]
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[4.17, 489] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF502IPK.bed.gz | 285.34 KB | 94f59d1843f85d07290903fc9c460a2a |
| ENCFF502IPK.bed.gz.dvc | 100.0 B | 3d39bd1d6917e56cdfbf3d7339cbbbb6 |
| ENCFF502IPK.tabix.bed.gz | 219.42 KB | b2a7532a08383040566ef28adce13dec |
| ENCFF502IPK.tabix.bed.gz.dvc | 106.0 B | 420a3115b5481eab4ef07e065280e73c |
| ENCFF502IPK.tabix.bed.gz.tbi | 104.04 KB | 49dca8d7e2bbcc2f5ff5a0cdb317b941 |
| ENCFF502IPK.tabix.bed.gz.tbi.dvc | 110.0 B | 56de2e03a2fcdd63f27a76aee9eb0336 |
| genomic_resource.yaml | 4.2 KB | 5112c80a4a007a65a6cc013ede6100bd |
| genomic_resource_original.yaml | 4.1 KB | 28792612147bf5b596606da7bb25d5de |
| statistics/ |