TF_ChIP-seq_ENCSR000DYP
TF_ChIP-seq ENCSR000DYP [biosample_summary="Homo sapiens GM12878" and target="ZNF384"]
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| Id: | TF_ChIP-seq/ENCSR000DYP |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000DYP [biosamplesummary="Homo sapiens GM12878" and target="ZNF384"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF942MDT|/files/ENCFF942MDT/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN623IOS|/analyses/ENCAN623IOS/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF055QMP|/files/ENCFF055QMP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18748729 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ZNF384-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 {ENCFF230KKA|/files/ENCFF230KKA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17342870 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ZNF384-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 {ENCFF230KKA|/files/ENCFF230KKA/} processed by ChIP-seq ENCODE3 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 {ENCFF230KKA|/files/ENCFF230KKA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.67. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF909FAL|/files/ENCFF909FAL/}, {ENCFF188SDF|/files/ENCFF188SDF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.33 and a self consistency ratio of 15.96. 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 {ENCFF324LIJ|/files/ENCFF324LIJ/}, {ENCFF942MDT|/files/ENCFF942MDT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.33 and a self consistency ratio of 15.96. 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_ENCSR000DYP | float |
TF_ChIP-seq_ENCSR000DYP |
TF_ChIP-seq ENCSR000DYP [biosample_summary="Homo sapiens GM12878" and target="ZNF384"]
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[6.76, 568] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF942MDT.bed.gz | 251.79 KB | 0d313660b213facd5683cf5baf9b9190 |
| ENCFF942MDT.bed.gz.dvc | 100.0 B | e5e49d9ba296fbf32af5364629b8d81b |
| ENCFF942MDT.tabix.bed.gz | 175.09 KB | db8633cc35bd6ba959f8ecd2a237c0a9 |
| ENCFF942MDT.tabix.bed.gz.dvc | 106.0 B | 1d0e318fb5f705baaf4126421e1df511 |
| ENCFF942MDT.tabix.bed.gz.tbi | 101.62 KB | 15d6a7784a519707e7fb1a3a9c543c6c |
| ENCFF942MDT.tabix.bed.gz.tbi.dvc | 110.0 B | e9312dc7998030c1b990cc5ce61b897a |
| genomic_resource.yaml | 4.97 KB | 3608dc1f23281a5d3479110e4b8213da |
| genomic_resource_original.yaml | 4.87 KB | 55d8a6d14ce2f76c6e65988ee360456a |
| statistics/ |