TF_ChIP-seq_ENCSR540LPD
TF_ChIP-seq ENCSR540LPD [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZNF839" and target="ZNF839"]
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| Id: | TF_ChIP-seq/ENCSR540LPD |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR540LPD [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZNF839" and target="ZNF839"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens ZNF839 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN389AZB|/analyses/ENCAN389AZB/} has in progress subobject document {160dd838-0dd9-432e-8047-82d2571550d9|/documents/160dd838-0dd9-432e-8047-82d2571550d9/} audit_internal_action: Released analysis {ENCAN389AZB|/analyses/ENCAN389AZB/} has replaced subobject file {7e777427-ac2b-41ae-8a84-4ce227455730|/files/7e777427-ac2b-41ae-8a84-4ce227455730/} audit_internal_action: Released analysis {ENCAN389AZB|/analyses/ENCAN389AZB/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} 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 {ENCFF120QNA|/files/ENCFF120QNA/} processed by ChIP-seq ENCODE4 v1.4.0 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 {ENCFF120QNA|/files/ENCFF120QNA/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.13. 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 {ENCFF132LSZ|/files/ENCFF132LSZ/} processed by ChIP-seq ENCODE4 v1.4.0 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 {ENCFF132LSZ|/files/ENCFF132LSZ/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 8.92. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF332MPQ|/files/ENCFF332MPQ/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.69 and a self consistency ratio of 3.66. 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 {ENCFF481VFR|/files/ENCFF481VFR/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.69 and a self consistency ratio of 3.66. 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_ENCSR540LPD | float |
TF_ChIP-seq_ENCSR540LPD |
TF_ChIP-seq ENCSR540LPD [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens ZNF839" and target="ZNF839"]
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[9.66, 381] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF332MPQ.bed.gz | 146.19 KB | 027b222ef474243937a53edca67d30ab |
| ENCFF332MPQ.bed.gz.dvc | 100.0 B | 14971ea25c8eb3f5fc9a8e49b51993aa |
| ENCFF332MPQ.tabix.bed.gz | 110.98 KB | 2f3efd5cada495ba9ea8ff4ef9c43e47 |
| ENCFF332MPQ.tabix.bed.gz.dvc | 106.0 B | 6a90a0ca1a9eff2f36759a14c5a3b74b |
| ENCFF332MPQ.tabix.bed.gz.tbi | 57.64 KB | 2c0c5007b2c4e5292d066b84d216dcc3 |
| ENCFF332MPQ.tabix.bed.gz.tbi.dvc | 109.0 B | af89bc44288bf819e507e5889690bbb6 |
| genomic_resource.yaml | 5.69 KB | 1b6b6bcd776d622f9c86f13d3faba955 |
| genomic_resource_original.yaml | 5.53 KB | 127c91815487002f2971fbe4d090ec9c |
| statistics/ |