TF_ChIP-seq_ENCSR813QEO
TF_ChIP-seq ENCSR813QEO [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens DPF2" and target="DPF2"]
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| Id: | TF_ChIP-seq/ENCSR813QEO |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR813QEO [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens DPF2" and target="DPF2"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens DPF2 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN086WQB|/analyses/ENCAN086WQB/} has in progress subobject document {a671dc0e-935f-497f-a281-7e4564a57441|/documents/a671dc0e-935f-497f-a281-7e4564a57441/} audit_internal_action: Released analysis {ENCAN086WQB|/analyses/ENCAN086WQB/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF435HBD|/files/ENCFF435HBD/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 19479487 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting DPF2-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 {ENCFF844EJA|/files/ENCFF844EJA/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 18316864 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting DPF2-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 {ENCFF435HBD|/files/ENCFF435HBD/} processed by ChIP-seq ENCODE4 v1.4.0 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 {ENCFF435HBD|/files/ENCFF435HBD/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.33. 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 {ENCFF844EJA|/files/ENCFF844EJA/} processed by ChIP-seq ENCODE4 v1.4.0 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 {ENCFF844EJA|/files/ENCFF844EJA/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.63. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF007COI|/files/ENCFF007COI/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.13 and a self consistency ratio of 2.00. 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 {ENCFF700HHQ|/files/ENCFF700HHQ/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.13 and a self consistency ratio of 2.00. 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_ENCSR813QEO | float |
TF_ChIP-seq_ENCSR813QEO |
TF_ChIP-seq ENCSR813QEO [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens DPF2" and target="DPF2"]
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[6.79, 281] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF007COI.bed.gz | 259.92 KB | 26c9d2065ba93d9a2502f7d5e4d9664b |
| ENCFF007COI.bed.gz.dvc | 100.0 B | cf0233d31c8972b63521aafc1faa2e60 |
| ENCFF007COI.tabix.bed.gz | 200.19 KB | ce324374c7b9aff05c0f4bcdeeb6c312 |
| ENCFF007COI.tabix.bed.gz.dvc | 106.0 B | 8ea287ba5fc284355e0fe891df3d4497 |
| ENCFF007COI.tabix.bed.gz.tbi | 95.73 KB | 1a35c60378428ed9aec861d7fddc6ea9 |
| ENCFF007COI.tabix.bed.gz.tbi.dvc | 109.0 B | f2cb290f3d7aafa521d12afb01341b62 |
| genomic_resource.yaml | 6.44 KB | e9807fafff267b269ada80e5f249f93b |
| genomic_resource_original.yaml | 6.28 KB | f2afcdaceacf70a2760a4808c2baad79 |
| statistics/ |