TF_ChIP-seq_ENCSR799DUB
TF_ChIP-seq ENCSR799DUB [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens IKZF4" and target="IKZF4"]
×
| Id: | TF_ChIP-seq/ENCSR799DUB |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR799DUB [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens IKZF4" and target="IKZF4"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens IKZF4 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN959VZI|/analyses/ENCAN959VZI/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN959VZI|/analyses/ENCAN959VZI/} has in progress subobject document {f4f145c9-c17b-49db-82c3-e66ff6327a3a|/documents/f4f145c9-c17b-49db-82c3-e66ff6327a3a/} audit_warning: Processed alignments file {ENCFF275EDJ|/files/ENCFF275EDJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 17697695 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting IKZF4-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 {ENCFF601ZSJ|/files/ENCFF601ZSJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF601ZSJ|/files/ENCFF601ZSJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.72. 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 {ENCFF275EDJ|/files/ENCFF275EDJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF275EDJ|/files/ENCFF275EDJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.82. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF948XVV|/files/ENCFF948XVV/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.40 and a self consistency ratio of 4.96. 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. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF823YYW|/files/ENCFF823YYW/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline have a rescue ratio of 1.40 and a self consistency ratio of 4.96. 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: |
|
| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR799DUB | float |
TF_ChIP-seq_ENCSR799DUB |
TF_ChIP-seq ENCSR799DUB [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens IKZF4" and target="IKZF4"]
|
|
[8.25, 479] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF948XVV.bed.gz | 182.3 KB | 3eaaf662a612e23eeeb85ad29a3a8afe |
| ENCFF948XVV.bed.gz.dvc | 100.0 B | c006f2fd1ba187aff8fb598af8bd7737 |
| ENCFF948XVV.tabix.bed.gz | 136.8 KB | 52cf6411c5bad76e8a87fd01b2a71b85 |
| ENCFF948XVV.tabix.bed.gz.dvc | 106.0 B | afbab377eb8dacbd85a3dee5a720199b |
| ENCFF948XVV.tabix.bed.gz.tbi | 65.84 KB | 6cf8b87f5a1b82b57c6eb09671b1e809 |
| ENCFF948XVV.tabix.bed.gz.tbi.dvc | 109.0 B | c6c60a7dcaf0d5a6879c4fd2fc422057 |
| genomic_resource.yaml | 5.97 KB | 6bc4e6bd7b92c7371771621006cd90dd |
| genomic_resource_original.yaml | 5.81 KB | 8471e7463c862b17da0f693dd5a1c275 |
| statistics/ |