| Id: | TF_ChIP-seq/ENCSR539PMH |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR539PMH [biosamplesummary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens CENPBD1" and target="CENPBD1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: genetically modified (insertion) using CRISPR targeting H. sapiens CENPBD1 output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN103QZH|/analyses/ENCAN103QZH/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF274HCD|/files/ENCFF274HCD/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 18014489 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CENPBD1-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 {ENCFF274HCD|/files/ENCFF274HCD/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF274HCD|/files/ENCFF274HCD/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.95. 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 {ENCFF385KXT|/files/ENCFF385KXT/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF385KXT|/files/ENCFF385KXT/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.67. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF456EDK|/files/ENCFF456EDK/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline have a rescue ratio of 1.99 and a self consistency ratio of 4.47. 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_ENCSR539PMH | float |
TF_ChIP-seq_ENCSR539PMH |
TF_ChIP-seq ENCSR539PMH [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens CENPBD1" and target="CENPBD1"]
|
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[9.56, 337] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF456EDK.bed.gz | 52.86 KB | eb971a8abacb92c6c55f35966038cd4f |
| ENCFF456EDK.bed.gz.dvc | 99.0 B | f0bb9c2bcbfd7ebf09f5c04fff81464d |
| ENCFF456EDK.tabix.bed.gz | 38.82 KB | 7ed14ec9241aa3981512cf1f17c513c1 |
| ENCFF456EDK.tabix.bed.gz.dvc | 105.0 B | 0abd83120b70529d8b048579831a2c9f |
| ENCFF456EDK.tabix.bed.gz.tbi | 25.72 KB | eb1f28a3b59066d16a9f3cecaf6e3ec0 |
| ENCFF456EDK.tabix.bed.gz.tbi.dvc | 109.0 B | 7a2c810b2348c435b24a998d3ac41e7c |
| genomic_resource.yaml | 5.25 KB | 3daab4054e89107ad7ec2ce475a34466 |
| genomic_resource_original.yaml | 5.09 KB | a3ed0338e0af12d150c226cb65c34768 |
| statistics/ |