TF_ChIP-seq_ENCSR000DVQ
TF_ChIP-seq ENCSR000DVQ [biosample_summary="Homo sapiens fibroblast of villous mesenchyme" and target="CTCF"]
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| Id: | TF_ChIP-seq/ENCSR000DVQ |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR000DVQ [biosamplesummary="Homo sapiens fibroblast of villous mesenchyme" and target="CTCF"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN072MHV|/analyses/ENCAN072MHV/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF976BRM|/files/ENCFF976BRM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 9125871 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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 {ENCFF569PMD|/files/ENCFF569PMD/} processed by ChIP-seq ENCODE3 hg19 pipeline has 12038868 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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 {ENCFF976BRM|/files/ENCFF976BRM/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF976BRM|/files/ENCFF976BRM/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.95. 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 {ENCFF569PMD|/files/ENCFF569PMD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF569PMD|/files/ENCFF569PMD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.95. |
| Labels: |
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| ID | Type | Default annotation | Description | Histogram | Range |
|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000DVQ | float |
TF_ChIP-seq_ENCSR000DVQ |
TF_ChIP-seq ENCSR000DVQ [biosample_summary="Homo sapiens fibroblast of villous mesenchyme" and target="CTCF"]
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[3.1, 573] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF738CXX.bed.gz | 750.48 KB | 5a3c9d8e93fc9918892fa2f3ecf1426a |
| ENCFF738CXX.bed.gz.dvc | 100.0 B | dea88b621bbc2850201f7b0b95c50c3a |
| ENCFF738CXX.tabix.bed.gz | 574.67 KB | e65dd647542827b5394398d2e0d99d50 |
| ENCFF738CXX.tabix.bed.gz.dvc | 106.0 B | a7daa1d84ab88fde423c419859df2ac5 |
| ENCFF738CXX.tabix.bed.gz.tbi | 292.93 KB | eacbb4f925c9bd60b37354fe9b6b48ee |
| ENCFF738CXX.tabix.bed.gz.tbi.dvc | 110.0 B | 9cff6a2ae0d7b8c8028205ff305143e6 |
| genomic_resource.yaml | 5.31 KB | 0b9efdf4a3946dd69d38c80d460b978b |
| genomic_resource_original.yaml | 5.2 KB | 9b65e642262105afefcfc8748e31a447 |
| statistics/ |