TF_ChIP-seq_ENCSR364SNE
TF_ChIP-seq ENCSR364SNE [biosample_summary="Homo sapiens K562" and target="POU5F1"]
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| Id: | TF_ChIP-seq/ENCSR364SNE |
| Type: | position_score |
| Version: | 0 |
| Summary: |
TFChIP-seq ENCSR364SNE [biosamplesummary="Homo sapiens K562" and target="POU5F1"] |
| Description: |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN528JZJ|/analyses/ENCAN528JZJ/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_internal_action: File {ENCFF814QPF|/files/ENCFF814QPF/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_warning: Processed alignments file {ENCFF645RWA|/files/ENCFF645RWA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13009789 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting POU5F1-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 {ENCFF178ZLZ|/files/ENCFF178ZLZ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18070269 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting POU5F1-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 {ENCFF645RWA|/files/ENCFF645RWA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF645RWA|/files/ENCFF645RWA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.47. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF692JCC|/files/ENCFF692JCC/}, {ENCFF814QPF|/files/ENCFF814QPF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.49 and a self consistency ratio of 3.76. 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 {ENCFF037CCA|/files/ENCFF037CCA/}, {ENCFF208QKB|/files/ENCFF208QKB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.49 and a self consistency ratio of 3.76. 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_ENCSR364SNE | float |
TF_ChIP-seq_ENCSR364SNE |
TF_ChIP-seq ENCSR364SNE [biosample_summary="Homo sapiens K562" and target="POU5F1"]
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[4.38, 179] |
| Filename | Size | md5 |
|---|---|---|
| ENCFF814QPF.bed.gz | 37.92 KB | 6efe277e840603535c2d355e3e357386 |
| ENCFF814QPF.bed.gz.dvc | 99.0 B | 3b2030d3ac6d08b3e77878f81970d49e |
| ENCFF814QPF.tabix.bed.gz | 26.01 KB | 3b64d2a5b50b12282a06b64842a6f7e8 |
| ENCFF814QPF.tabix.bed.gz.dvc | 105.0 B | 71e40e1983dd31405531d13149327065 |
| ENCFF814QPF.tabix.bed.gz.tbi | 24.34 KB | 4c2888c93f978410b2348e7d6061b317 |
| ENCFF814QPF.tabix.bed.gz.tbi.dvc | 109.0 B | e97f2359c73b658903aa8e84ea593636 |
| genomic_resource.yaml | 5.51 KB | b55c31a18ac9e850d333cae4dd512934 |
| genomic_resource_original.yaml | 5.41 KB | 44d612e94db8aeddb4a54ee25daaf889 |
| statistics/ |