TF_ChIP-seq_ENCSR225OGU
TF_ChIP-seq ENCSR225OGU [biosample_summary="Homo sapiens K562 genetically modified (insertion) using CRISPR targeting H. sapiens ERF" and target="ERF"]
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| Id: | TF_ChIP-seq/ENCSR225OGU |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR225OGU [biosamplesummary="Homo sapiens K562 genetically modified (insertion) using CRISPR targeting H. sapiens ERF" and target="ERF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens ERF output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN412IVM|/analyses/ENCAN412IVM/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF969KAS|/files/ENCFF969KAS/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 18997336 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ERF-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 {ENCFF491DOB|/files/ENCFF491DOB/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 17857485 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ERF-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 {ENCFF969KAS|/files/ENCFF969KAS/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF969KAS|/files/ENCFF969KAS/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.40. 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 {ENCFF491DOB|/files/ENCFF491DOB/} processed by ChIP-seq ENCODE4 v1.8.0 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 {ENCFF491DOB|/files/ENCFF491DOB/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.84. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF330EGV|/files/ENCFF330EGV/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline have a rescue ratio of 1.37 and a self consistency ratio of 2.88. 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_ENCSR225OGU | float |
TF_ChIP-seq_ENCSR225OGU |
TF_ChIP-seq ENCSR225OGU [biosample_summary="Homo sapiens K562 genetically modified (insertion) using CRISPR targeting H. sapiens ERF" and target="ERF"]
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[6.93, 405] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF330EGV.bed.gz | 48.22 KB | 1aed2eba88c74f09e568a20949faa66d |
| ENCFF330EGV.bed.gz.dvc | 99.0 B | 8b03590ce0fa3da386649dc569e4d31e |
| ENCFF330EGV.tabix.bed.gz | 34.49 KB | d022e5cf8b49fa4cb2a02be4832cd82a |
| ENCFF330EGV.tabix.bed.gz.dvc | 105.0 B | 0fd2f1384a027061976315a9ccfc6e51 |
| ENCFF330EGV.tabix.bed.gz.tbi | 24.24 KB | 8afbde3aa32ad23864e7791ad55e4f0f |
| ENCFF330EGV.tabix.bed.gz.tbi.dvc | 109.0 B | 1b9a5ecdb2558915c2dca7837c96bd26 |
| genomic_resource.yaml | 5.7 KB | ce41737c502a722532000ff8e9b28d07 |
| genomic_resource_original.yaml | 5.54 KB | fb445486759ffb6e669b80ae97428d52 |
| statistics/ |