TF_ChIP-seq_ENCSR000DNN
TF_ChIP-seq ENCSR000DNN [biosample_summary="Homo sapiens GM12878" and target="NFYA"]
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| Id: | TF_ChIP-seq/ENCSR000DNN |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000DNN [biosamplesummary="Homo sapiens GM12878" and target="NFYA"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN790IWP|/analyses/ENCAN790IWP/} has in progress subobject document {6b9ef026-4f5b-44bc-a669-31a36e0528d6|/documents/6b9ef026-4f5b-44bc-a669-31a36e0528d6/} audit_internal_action: Released analysis {ENCAN790IWP|/analyses/ENCAN790IWP/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF797PCH|/files/ENCFF797PCH/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 10396865 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting NFYA-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 {ENCFF906LHW|/files/ENCFF906LHW/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 10840093 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting NFYA-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 {ENCFF906LHW|/files/ENCFF906LHW/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF906LHW|/files/ENCFF906LHW/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.04. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF937QTP|/files/ENCFF937QTP/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.46 and a self consistency ratio of 2.62. 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_ENCSR000DNN | float |
TF_ChIP-seq_ENCSR000DNN |
TF_ChIP-seq ENCSR000DNN [biosample_summary="Homo sapiens GM12878" and target="NFYA"]
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[4.85, 194] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF937QTP.bed.gz | 17.51 KB | 2da4bf1a32c700d20bf803320c9d2986 |
| ENCFF937QTP.bed.gz.dvc | 99.0 B | 18a7e4570b51186d79951a04c288cf42 |
| ENCFF937QTP.tabix.bed.gz | 12.49 KB | 353615f38eaab991af934588fc033b2e |
| ENCFF937QTP.tabix.bed.gz.dvc | 105.0 B | d733bf6ebed14fc4512cbdacdb56f64f |
| ENCFF937QTP.tabix.bed.gz.tbi | 14.46 KB | 047af1dffeb8a371ac4318b53256fb54 |
| ENCFF937QTP.tabix.bed.gz.tbi.dvc | 109.0 B | 8515c50e372cd9387e8f10770d9f28eb |
| genomic_resource.yaml | 4.42 KB | 97a2b9e2e3e4eb27479aa8b8cd234689 |
| genomic_resource_original.yaml | 4.32 KB | c3642c2f8e7587f73ca20fddff6b0187 |
| statistics/ |