TF_ChIP-seq_ENCSR000ARD
TF_ChIP-seq ENCSR000ARD [biosample_summary="Homo sapiens GM12878" and target="EZH2"]
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| Id: | TF_ChIP-seq/ENCSR000ARD |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000ARD [biosamplesummary="Homo sapiens GM12878" and target="EZH2"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN652RAB|/analyses/ENCAN652RAB/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF689FFZ|/files/ENCFF689FFZ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 9635069 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting EZH2-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 {ENCFF689FFZ|/files/ENCFF689FFZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF689FFZ|/files/ENCFF689FFZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.36. 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 {ENCFF385WMX|/files/ENCFF385WMX/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF385WMX|/files/ENCFF385WMX/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.73. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF134RHC|/files/ENCFF134RHC/}, {ENCFF413QYZ|/files/ENCFF413QYZ/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.03 and a self consistency ratio of 3.83. 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 {ENCFF437BUE|/files/ENCFF437BUE/}, {ENCFF678JII|/files/ENCFF678JII/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.03 and a self consistency ratio of 3.83. 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_ENCSR000ARD | float |
TF_ChIP-seq_ENCSR000ARD |
TF_ChIP-seq ENCSR000ARD [biosample_summary="Homo sapiens GM12878" and target="EZH2"]
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[7.54, 171] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF678JII.bed.gz | 36.32 KB | e89a61b52a33a3db505994d17393df9a |
| ENCFF678JII.bed.gz.dvc | 99.0 B | 63b75d40fbc8a99bfd1e10d76eb510a4 |
| ENCFF678JII.tabix.bed.gz | 23.73 KB | e1bb8ff7e2740e0077006f1e2ca4db3d |
| ENCFF678JII.tabix.bed.gz.dvc | 105.0 B | 0e3642f4cb9b929021209c0975163935 |
| ENCFF678JII.tabix.bed.gz.tbi | 18.88 KB | 887b76b40ac79d712bd4fce1fa65e19f |
| ENCFF678JII.tabix.bed.gz.tbi.dvc | 109.0 B | 333dbb0ce37281281548a36dd40f85ac |
| genomic_resource.yaml | 5.58 KB | 8def5103a4f4fc56a77ca09a54591c4d |
| genomic_resource_original.yaml | 5.48 KB | 29cd1de47659f12371be8518460cc8fb |
| statistics/ |