TF_ChIP-seq_ENCSR868JLS
TF_ChIP-seq ENCSR868JLS [biosample_summary="Homo sapiens HepG2" and target="U2AF1"]
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| Id: | TF_ChIP-seq/ENCSR868JLS |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR868JLS [biosamplesummary="Homo sapiens HepG2" and target="U2AF1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Released analysis {ENCAN587ACX|/analyses/ENCAN587ACX/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_internal_action: File {ENCFF034KUO|/files/ENCFF034KUO/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_warning: Processed alignments file {ENCFF881XYD|/files/ENCFF881XYD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13390753 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting U2AF1-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 {ENCFF740GLK|/files/ENCFF740GLK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15822761 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting U2AF1-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 {ENCFF881XYD|/files/ENCFF881XYD/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF881XYD|/files/ENCFF881XYD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.36. 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 {ENCFF740GLK|/files/ENCFF740GLK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.98. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF886AIM|/files/ENCFF886AIM/}, {ENCFF034KUO|/files/ENCFF034KUO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.23 and a self consistency ratio of 2.15. 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 {ENCFF190TFD|/files/ENCFF190TFD/}, {ENCFF548XGJ|/files/ENCFF548XGJ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.23 and a self consistency ratio of 2.15. 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_ENCSR868JLS | float |
TF_ChIP-seq_ENCSR868JLS |
TF_ChIP-seq ENCSR868JLS [biosample_summary="Homo sapiens HepG2" and target="U2AF1"]
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[5.66, 121] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF034KUO.bed.gz | 115.31 KB | 0886519e60906a7f5ff4574a84860568 |
| ENCFF034KUO.bed.gz.dvc | 100.0 B | 8d7ba9b4237ed4b0bcad79fb86a0b33b |
| ENCFF034KUO.tabix.bed.gz | 93.78 KB | 4c841933a58eb2f2ce018ddc17bb775d |
| ENCFF034KUO.tabix.bed.gz.dvc | 105.0 B | 35c8c12b4241d905ea300b98363f303c |
| ENCFF034KUO.tabix.bed.gz.tbi | 47.04 KB | 2f92e59d83f36829dd2be6bc425d34cf |
| ENCFF034KUO.tabix.bed.gz.tbi.dvc | 109.0 B | cd6771235a5a4c573a1e2415e1f2d14a |
| genomic_resource.yaml | 5.59 KB | c029edb8def0b21c0fdf296c38994862 |
| genomic_resource_original.yaml | 5.5 KB | 40faf232e17b4cbd4c3679ed6c86e0b9 |
| statistics/ |