TF_ChIP-seq_ENCSR000BKK
TF_ChIP-seq ENCSR000BKK [biosample_summary="Homo sapiens H1" and target="EP300"]
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| Id: | TF_ChIP-seq/ENCSR000BKK |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000BKK [biosamplesummary="Homo sapiens H1" and target="EP300"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN886QCD|/analyses/ENCAN886QCD/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF060WKJ|/files/ENCFF060WKJ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 10318720 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting EP300-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 {ENCFF123VAK|/files/ENCFF123VAK/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17866580 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting EP300-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 {ENCFF060WKJ|/files/ENCFF060WKJ/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF060WKJ|/files/ENCFF060WKJ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.90. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF843SYD|/files/ENCFF843SYD/}, {ENCFF087TMV|/files/ENCFF087TMV/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.46 and a self consistency ratio of 8.16. 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 {ENCFF872MGS|/files/ENCFF872MGS/}, {ENCFF015SPK|/files/ENCFF015SPK/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.46 and a self consistency ratio of 8.16. 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_ENCSR000BKK | float |
TF_ChIP-seq_ENCSR000BKK |
TF_ChIP-seq ENCSR000BKK [biosample_summary="Homo sapiens H1" and target="EP300"]
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[4.65, 288] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF843SYD.bed.gz | 235.97 KB | c06ac8027f55d91b669cebbc14184c53 |
| ENCFF843SYD.bed.gz.dvc | 100.0 B | 0f8ad27a18e2138bda002935eb5d862f |
| ENCFF843SYD.tabix.bed.gz | 162.88 KB | 99a499656a74972c144559c2b762b0a6 |
| ENCFF843SYD.tabix.bed.gz.dvc | 106.0 B | d8adbadf344211b832d3891c22e8b7af |
| ENCFF843SYD.tabix.bed.gz.tbi | 105.96 KB | 43d50d732f9509477695b62500a623a6 |
| ENCFF843SYD.tabix.bed.gz.tbi.dvc | 110.0 B | 0a83594d981ab2cedbd17e11e898edeb |
| genomic_resource.yaml | 4.76 KB | 2bb4d5f86b385751d98e6b767b6212a8 |
| genomic_resource_original.yaml | 4.66 KB | 495e692890284ae3facd9e56c8c4e2fe |
| statistics/ |