TF_ChIP-seq_ENCSR362CPB
TF_ChIP-seq ENCSR362CPB [biosample_summary="Homo sapiens HepG2" and target="HDAC1"]
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| Id: | TF_ChIP-seq/ENCSR362CPB |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR362CPB [biosamplesummary="Homo sapiens HepG2" and target="HDAC1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN233ARC|/analyses/ENCAN233ARC/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF524KPD|/files/ENCFF524KPD/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 19691150 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting HDAC1-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 {ENCFF524KPD|/files/ENCFF524KPD/} processed by ChIP-seq ENCODE4 v1.7.0 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 {ENCFF524KPD|/files/ENCFF524KPD/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 8.82. 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 {ENCFF653KFT|/files/ENCFF653KFT/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 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 {ENCFF653KFT|/files/ENCFF653KFT/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 8.60. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF133VHU|/files/ENCFF133VHU/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline have a rescue ratio of 1.67 and a self consistency ratio of 5.00. 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_ENCSR362CPB | float |
TF_ChIP-seq_ENCSR362CPB |
TF_ChIP-seq ENCSR362CPB [biosample_summary="Homo sapiens HepG2" and target="HDAC1"]
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[6.82, 231] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF133VHU.bed.gz | 337.84 KB | b0b7e67a714b61be26ff0662c8dccfb5 |
| ENCFF133VHU.bed.gz.dvc | 100.0 B | b01be39c37603945dac7c5fe4bc1aa66 |
| ENCFF133VHU.tabix.bed.gz | 285.43 KB | 68132064e7b219bb53fc920089f7e08d |
| ENCFF133VHU.tabix.bed.gz.dvc | 106.0 B | ac99c9566793c6b29824130ea3c1b421 |
| ENCFF133VHU.tabix.bed.gz.tbi | 95.4 KB | c44701ee38f6315a9fbc272958eec7dc |
| ENCFF133VHU.tabix.bed.gz.tbi.dvc | 109.0 B | 57b59647aacaa5d49ea4dbc3795cbd87 |
| genomic_resource.yaml | 5.01 KB | 77f75c0d524b4b137beefa771d08a4b9 |
| genomic_resource_original.yaml | 4.92 KB | 8155401cb5f7511c2fe56ff9d2bf6997 |
| statistics/ |