TF_ChIP-seq_ENCSR902AMJ
TF_ChIP-seq ENCSR902AMJ [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZNF660" and target="ZNF660"]
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| Id: | TF_ChIP-seq/ENCSR902AMJ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR902AMJ [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZNF660" and target="ZNF660"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens ZNF660 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN103HYQ|/analyses/ENCAN103HYQ/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN103HYQ|/analyses/ENCAN103HYQ/} has in progress subobject document {2ae5eae9-5743-4493-80a6-6e400ba41b4a|/documents/2ae5eae9-5743-4493-80a6-6e400ba41b4a/} audit_warning: Processed alignments file {ENCFF883EWV|/files/ENCFF883EWV/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 19571325 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ZNF660-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 {ENCFF281FTT|/files/ENCFF281FTT/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 19656317 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ZNF660-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 {ENCFF883EWV|/files/ENCFF883EWV/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF883EWV|/files/ENCFF883EWV/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.88. 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 {ENCFF281FTT|/files/ENCFF281FTT/} 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 {ENCFF281FTT|/files/ENCFF281FTT/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.59. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF215UIS|/files/ENCFF215UIS/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.96 and a self consistency ratio of 4.57. 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_ENCSR902AMJ | float |
TF_ChIP-seq_ENCSR902AMJ |
TF_ChIP-seq ENCSR902AMJ [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZNF660" and target="ZNF660"]
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[6.24, 309] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF215UIS.bed.gz | 26.69 KB | 176f97d3e32fc9d328050024c9a8958a |
| ENCFF215UIS.bed.gz.dvc | 99.0 B | c1e13c1b56452bd45004878ab1e0fe00 |
| ENCFF215UIS.tabix.bed.gz | 20.24 KB | 524bb66a48adafb85c81a2f6a31830e4 |
| ENCFF215UIS.tabix.bed.gz.dvc | 105.0 B | 2cfdc2bb1a24c02bc053633380b358e9 |
| ENCFF215UIS.tabix.bed.gz.tbi | 16.7 KB | b506ab1d5b08e941f2d7f816ad472b6e |
| ENCFF215UIS.tabix.bed.gz.tbi.dvc | 109.0 B | 4f98578cb0b794b4c6b34c17bd4db1e4 |
| genomic_resource.yaml | 5.94 KB | b46e5fff707941a7f0af1538cbda67e0 |
| genomic_resource_original.yaml | 5.78 KB | 486c11ed6c2249a6f80d9c21f0be3e6a |
| statistics/ |