TF_ChIP-seq_ENCSR793EHQ
TF_ChIP-seq ENCSR793EHQ [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens HNF4G" and target="HNF4G"]
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| Id: | TF_ChIP-seq/ENCSR793EHQ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR793EHQ [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens HNF4G" and target="HNF4G"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens HNF4G output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN491AKJ|/analyses/ENCAN491AKJ/} has in progress subobject document {28b32261-8042-4b6c-b4a0-310db205c1eb|/documents/28b32261-8042-4b6c-b4a0-310db205c1eb/} audit_internal_action: Released analysis {ENCAN491AKJ|/analyses/ENCAN491AKJ/} has replaced subobject file {996a315f-6410-45b4-8e68-506ed5d164e1|/files/996a315f-6410-45b4-8e68-506ed5d164e1/} audit_internal_action: Released analysis {ENCAN491AKJ|/analyses/ENCAN491AKJ/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN491AKJ|/analyses/ENCAN491AKJ/} has replaced subobject file {ed15cf35-95a0-4b1f-8c7b-1897167d3101|/files/ed15cf35-95a0-4b1f-8c7b-1897167d3101/} audit_warning: Processed alignments file {ENCFF186NSM|/files/ENCFF186NSM/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 19318404 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting HNF4G-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 {ENCFF186NSM|/files/ENCFF186NSM/} 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 {ENCFF186NSM|/files/ENCFF186NSM/} processed by ChIP-seq ENCODE4 v1.4.0 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 {ENCFF067TCZ|/files/ENCFF067TCZ/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF067TCZ|/files/ENCFF067TCZ/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 8.14. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF413UQM|/files/ENCFF413UQM/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.32 and a self consistency ratio of 2.91. 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 {ENCFF150UPI|/files/ENCFF150UPI/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.32 and a self consistency ratio of 2.91. 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_ENCSR793EHQ | float |
TF_ChIP-seq_ENCSR793EHQ |
TF_ChIP-seq ENCSR793EHQ [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens HNF4G" and target="HNF4G"]
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[7.99, 332] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF413UQM.bed.gz | 275.34 KB | e24ae59c266835b35711b95e89dd8c8d |
| ENCFF413UQM.bed.gz.dvc | 100.0 B | 0e6f5212ed0c5c3db5db797d5d1a98b7 |
| ENCFF413UQM.tabix.bed.gz | 216.74 KB | af58d54140edf4b69817b0a30e75d425 |
| ENCFF413UQM.tabix.bed.gz.dvc | 106.0 B | 5ba7199aab755431be2cca2bcd0419aa |
| ENCFF413UQM.tabix.bed.gz.tbi | 100.18 KB | c23f81637f8cb6edb775c8d867d1d4b0 |
| ENCFF413UQM.tabix.bed.gz.tbi.dvc | 110.0 B | a2c92d108de259eebb53130d45211e7a |
| genomic_resource.yaml | 6.37 KB | 7e663a3d4715d2758e510f448c4c229e |
| genomic_resource_original.yaml | 6.21 KB | 5f2751f3b562c856fe1c5d05093c7ab7 |
| statistics/ |